Mass Impact 2
by Quietness731
Summary: It's been several months, and now the Reapers are here. But is the knowledge of the future really enough to save everyone? OC insert, most of the visual details are ambiguous and up to the reader, but the armor is already predetermined. Sequel to Mass Impact.
1. Chapter 1: Conveniently

Tom looked at the camera footage that he had 'borrowed' from the mainframe of the facility. Docter Eva had just murdered two security guards right there. Shame she didn't realize that someone else was watching her. He was in a side room that handled the servers of the mars archives, giving himself access had never been easier. He switched the camera feed when Eva shot the camera, the camera he switched to was looking at the area outside his door..

He watched as a scientist ran down the hallway, rushing past his door and attempting to gain access to the room with the turret, but he fumbled with his key card and got shot before he could pick it up, Tom cringed.

 _It's a necessary casualty_ he reminded himself, the ruthless calculus of war was a bit more ruthless then he wanted to believe.

"Confirmed kill, move onto primary objective." A centurion said before popping the heat sink on his Mattock.

"Sir yes sir!" He wanted to go out there and kill them all, but he restrained himself, the time would come after all.

"Sir, we have several hostiles engaging our operatives through that door to the right, ID has confirmed that Shepard is among them, orders?"

"Secure the auto turret as confirmed in the building's schematics, we'll stop Shepard from there."

"Sir yes sir!" The Cerberus troops took the key card and opened the door, predictably entering the control room where the automated gun was controlled from.

XXXXXXXXXXXXXX

"Shepard, they have a heavy auto turret ahead of us, that thing'll tear your shields down in an instant!" Liara yelled, before immediately rolling into cover.

"Sprint from cover to cover as fast as you can, we'll bypass that thing eventually!" Shepard shouted before sprinting right to the next area that provided enough cover to shield him from the turret, the thing had halved his shields in just the several seconds he was out of cover.

"Shepard, there's no cover at the end of the hallway, what are we supposed to do?!" Kaiden shouted.

"We'll deal with that when we get there I-" Shepard was cut off by a commotion in the control room, they couldn't take a peek because they'd have their heads taken off in an instant, but it sounded like several people were screaming in there, in particular were the screams of Cerberus troops.

"What's going on in there?" Shepard doubted that Liara or himself would have the answer to that, unless he found out for himself.

"Looks someone else also wants them dead." Kaiden observed.

"Let's take advantage of this, keep moving from cover to cover, let's see what's going on." Shepard ordered.

After moving from cover a bit everyone realized that the gun was offline, so they all just booked it until they were out of the sight line of the gun.

There were several gunshots heard as someone was executed, the smoke was still clearing up so no one could see what was happening, nor who was winning, but at this point the Cerberus troops were proably all dead, judging by the screams from earlier.

"Wait for the smoke to clear, we have no idea who's winning." Shepard pulled out his shotgun, ready to go guns blazing.

"Who do you think won?" Liara asked.

"I have no clue, we'll find out soon." Kaiden said.

"Cerberus is dead, you can come in, Commander Shepard." The voice sounded synthesized.

"Why the hell should I trust you? Sure you did take care of the guards, but that doesn't mean I'm already your friend."

"Because I'm already your friend, let me take off my helmet." The man took off his helmet. "Do you recognize my voice now? You better not have developed amnesia because I didn't fight along side you on the suicide mission just so that you could forget me."

Shepard was struck dumb. "Tom? Why the hell are you here?"

"I got bored, plus Liara here was doing interesting research, and since I was free to work I decide to be 'hired' as a security guard, but not really. The network here was easy enough to hack into, since around 2 months to ensure that no one would be suspicious of my presence, I can hack anything with enough time."

"That's it? You seem to be here for some other reasons as well."

"Well, I guess the odds were in my favor of meeting up with you, let's get going now though, there some Cerberus goons we need to kill."

"I don't know you, were you actually one of the security guards working here? How did you manage to get past our top of the line cyber security?"

"Liara, like I said earlier I can crack any security system, and you were too into your research to really notice me, and plus I was never patrolling your section anyway, let's just get to archives."

"He's right Liara, can you get us over there?"

Liara ran over to the console and and tapped on a couple buttons.

"No, it's on a separate network, we're completely locked out."

"Amateurs, I'm pretty sure Tali could get past this." Tom said before pushing her aside and entering several console commands, which forced the tram to come back to the docking point.

"How did you do that?"

"Hey, I snuck a virus on there beforehand, this stuff is easy for me."

"Should we be expecting anyone?" Shepard asked.

"I've seen the cams on the tram, no one is there, we can go on through."

"Alright, with that aside, are you coming with us Tom?"

"Hell yes! The last couple months were pretty dull, and trouble seems to follow you everywhere, I'm right behind you."

Shepard grinned, THIS was the Fisher he knew.

...

"Those stupids over there have decided to come with a tram to kill us, but this also allows to to board theirs and go all the way to the other entrance without anymore explosives."

"How many of these guys have you killed again, Tom?"

"The ones you saw me stab, we got incoming!"

Tom ducked as a rain of gunfire erupted over his head, after they ran out of ammo he popped out of cover and nailed one of them with his Widow sniper. Then Liara used a singularity, which was then followed by a reave from Kaiden which resulted in a biotic detonation.

"Good going, keep moving." Shepard and co. hopped from the broken tram to the fixed tram, which Tom activated.

"That was pretty neat, I wish I had biotics." Tom said.

"It's a blessing/curse for me, those migraines really are a killer sometimes."

"Are you an L2?"

"Yeah, it's worth the pain, said biotics have saved me several times in multiple gunfights."

"Cut the chatter! We got hostiles ahead."

Shepard quickly jumped out of the tram, shot two Cerberus troops in two perfect head shots, before hopping into cover

 _What a showoff._ Tom thought, mentally smirking. Someone was putting points in the adrenaline ability.

"Ugh, I hate these guys!" Kaiden shouted as he tried to shoot a Guardian, the effort proving futile because of his shield.

"What are you talking about?" Shepard asked before throwing a grenade right behind the guy, blowing him up.

"You're lucky cause you have grenades."

Tom wasn't listening to their banter though as he had just pulled off the perfect head shot on a centurion.

He was about to celebrate, but a quarter of his shields got decimated by a guardian who had flanked him.

"On you're left!" Shepard shouted.

Tom mentally sighed when he saw the giant shield the guardian was behind, but the he ran up to the guy and shouted at him.

"I will shove this sniper down you're throat!" Before shoving the barrel of his widow down the 'mail slot' in the guardian's shield and blowing his head off.

"Gee, I didn't know you were such a crank shot, Fisher." Shepard teased.

"Hey, the closer they are, the less amount of effort I have to put in aiming my gun."

"Alright, I think they're all dead, let's grab the data on the prothean schematics and get the hell out of here." Shepard said before holstering his gun.

Shepard and co. entered the archives, which seemed pretty calm, a sharp contrast to the combat they had experienced in the past 20 minutes.

"Kaiden, Tom, sweep the room, Liara, on me."

Tom cut Dr. Eva's download and then quickly replaced it with junk data, shame she didn't know it.

"What are doing? Get moving." Kaiden said in a hurried tone.

"I'm right behind you, lead on."

"Shepard." Shepard turned around as soon as he heard that tone.

"What the hell are you doing here, you Illusive bastard?"

"I'm taking the schematics of the weapon that would assure humanity's ultimate domination over the reapers, and the rest of the galaxy." _Like hell he was_ Shepard thought.

"No chance in hell, asshole, shooting civilians is not acceptable, when is killing HUMAN civilians acceptable?"

"It's their sacrifice that lets us win the war, I'm assuring our rise to the peak of galactic society."

"That's stupid, why are you doing it NOW?! The reapers are tearing us apart, and all you're concerned about his making sure humans are on the top of society, your ideals sicken me, Liara, start the upload."

"Don't get in my way Shepard, you've already seen what I could do, you're in no position to take me down, let alone make empty threats."

"Upload has started Shepard, we should be done in about sixty seconds."

 _Meanwhile_

"Step away from the console." Kaiden said.

"No." Eva instantly turned around and threw him down, making him fumble for his gun. Tom instantly activated both of his Omni-blades and charged at her. He got in a total of one stab before he was incapacitated, and help by his neck in a bone crushing grip. He still had to work on his technique.

Shepard arrived on scene on that moment. "Put him down."

Eva ignored him. "Orders?" She asked to the Illusive man.

"Dispose of him."

But the order had come too late, as Shepard was already in the progress of smashing in Eve's stupid face. Tom only got minor lacerations on his neck from the vice grip that he was given earlier, nothing as serious as in the original games.

"Thanks for the assist, I thought I was done for." Tom said before kicking the deactivated android.

"What should we do with it?" Kaiden asked.

"Even though that thing was literally strangling me a second ago I think we should keep it, I might be able to get some stuff off of its data banks."

"As long as it doesn't come back to life it's fine by me, someone has to guard it though, Kaiden stay here and if this thing moves at all, shoot it, and then stick this grenade in its head, I don't want this to turn out like Sovereign did."

"Yes Commander." Kaiden said rigidly.

"Shepard, I'm having some issues here!" Liara said while frantically tapping on some buttons that controlled the prothean data banks.

Shepard rushed back to where Liara was. "What's going on?"

"Cerberus has initiated a data siphon, I can't stop it, I think Eva managed to give them an access point before Kaiden and Tom stopped her."

"Let me fix this, give me a couple of minutes." Tom said before quickly activating his Omni-tool and syncing it with the computer. "I think I'll be able to get this done with the help of a VI I had programmed over the past several months, although I'm not going to elaborate on the details any further, I got no time for explaining this."

"You're sure you'll be able to stop them?"

"I'm doing it now, but they have a huge amount of sources trying to siphon the data, they were only starting off when I stopped them, let's hope that the small amount of data they got wasn't important, but I can't get it back now."

"How long?"

"Hold that thought.." Tom said, he was in deep concentration. Pity he hadn't disabled Eve's download sooner, Cerberus had probably gotten the location of the prothean beacon on Liara's home planet now, but they didn't matter, he'd stop them later.

 _Several intense minutes later..._

"I got it! That was a bit too close for my liking, but I think I just shut off that last source." Tom wiped a small amount of sweat from his brow. That was one of the hardest tasks of cyber prowess he had ever completed.

"What do you mean when you say 'I think' did you get them all?" Shepard asked.

"I'm chec- wait WHAT?!" Tom looked at his Omni-tool, the words 'system infiltrated' were shown, glowing red on his Omni-tool.

"Shit, this is not good, I can't let them take my own data."

"What the hell is going on now?!"

"They've found my Omni-tool, they're deleting my data! Shit, they're deleting all of my hacking programs, shit, shit, fuck me, the only thing I've got left is my VI and a small amount of console commands, which they're locking me out of faster then I can type this shit in."

"Dang it, my system can't handle this, it wasn't built to handle an intrusion like this, I can't stop them, fuck, I shouldn't have let my guard down!" Why the hell were they hacking his own Omni-tool anyway?

"Is there anything I can do?" Liara asked.

"No, you wouldn't be able to connect, they've terminated anything I have on it that can connect to any other electronic, an- yep, there goes my VI they're deleting it now, and I can only hopelessly watch my months of hard work going down the drain in mere seconds."

Tom checked the statistics of his Omni-tool, his CPU was at 50% and decreasing due to the VI not taking much up after being slowly deleted, memory was going down due to the hacker deleting any run-times he had going on, and he had no connection, which is a stat he hadn't seen go down, due to there being wifi pretty much anywhere.

But for just a second Tom swore he saw the CPU spike to over 110% before the Omni-tool forced itself into a shutdown.

"Dang it!, I think that hacker or whoever was destroying all my things on this Omni-tool just put it into a forced shutdown, I had a lot of valuable stuff on it which I won't be getting back now, but nothing that will hinder me in terms of identity or anything related to that, good thing I had fail safes in place. Liara, did you at least get the data from the prothean data banks?"

"I got it all, thanks for stopping them. I think we should leave now, there's nothing else besides a lot of dead people here." Liara said the last part of her sentence with sadness in her tone.

"At least the mission objective is complete, Normandy, we're clear for pickup!"

"Roger that Shepard."

...

"What are going to do now that you have no Omni-tool Tom? The only thing you can use without it is your cloak, where are you going to get your tech powers from again?" Shepard asked.

"I'll probably buy a new Omni-tool and start fresh, I still know how to get those things on an Omni-tool at the very least, I still angry at the fact that they destroyed EVERYTHING on my Omni-tool, that VI was very very hard to code, and I don't want to make another one after this.

"Well, I'll buy you another one Omni-tool, you DID sacrifice it to get the prothean data, so you deserve that, among other things."

"Thanks for that, I still wish I had all of my old data, but I'll stop rambling for now, we have a Galaxy to go save."


	2. Chapter 2: Reality Check

It was a little while before they got back to the Normandy. But it was just like Tom had remembered it, it still had the exact interior as in the games, and he was glad that it hadn't changed one bit, Mass Effect 3 had his favorite version of the Normandy after all.

"So where am I supposed to put my gear this time? I guess the Alliance decided to do some renovations on the Normandy, right?" He asked, although he already every small detail about the ship, he was supposed to make this convincing.

"Follow me, we'll be taking our armor off down here, they moved the armor storage downstairs this time." Shepard said dismissively.

...

"They really stepped up their game with this Normandy didn't they?" Tom asked.

"Yeah, what was it like when Cerberus had it anyway?" Kaiden asked. He was supposed to give Tom a tour of the the ship on Shepard's orders.

"Well, there was too much yellow, have I mentioned that I really hated that color after the second Normandy? And we couldn't go down to the cargo bay unless we were going on a mission, I like the alliance blue much better then what Cerberus had going on, I glad we ditched the Illusive man after the Collector base, he was too nosy in everything we did and I hated that, but this isn't the time for me to discuss that, carry on."

Kaiden toured Tom around most of the ship, and it was a good hour before he actually managed to get settled into the bridge right next to Joker, just like he was on the previous Normandy.

"So you're already back again?" Joker asked.

"Of course, I was a little bored, and action follows Shepard all over the place, I decided it would be fun to hand out with him again, and I'm sure you guys needed me to secure the firewalls on this ship, it's about time I got back in this seat, it's also thoughtful of the Alliance to keep the leather padded chairs too."

"Finally someone else agrees with me! The seats on the original Normandy were the bane of my existence, and I'm glad the Alliance decided to keep these chairs, because I don't want to go back to the way it was before these seats.

"Wasn't the bane of your existence running? And or exercising? Just because of how fragile your bones are?"

"Oh right, that too, but I spend more time in a chair then I do on my feet so its much more of a pain if I have to sit in a seat made of stone." A that moment Shepard decided to stroll into the bridge.

"You've already gotten settled in?" Shepard asked.

"I'm an adaptable person Shepard, and since I've already been on your kind of ship before this, I know what to expect from you."

"And what exactly do you expect from serving on my ship again?"

"Alien diversity, a shit ton of ass kicking, and usually a beer at the bar on this ship after everything's all said and done and we got our reward for beating the bad guys."

"You really hit the nail on the head there, I couldn't of said it better myself." Shepard said before chuckling. "Now that the fun part is done, Joker I need you to set a course for the Citadel."

"Yes Commander, I'll set a course for their system now."

...

"I think I'm going to rest for a little bit, just before we get to the Citadel."

"I'll hold down the cockpit for a while, you can go rest."

"Thanks, see you later."

Tom walked out of the cockpit, went down the elevator to the crew deck, and then into the room where all the beds were. No one was there at the time the he decided to hit the hay. Since he was about to go to bed and since was a little curious, he decided to hit the power button on his Omni-tool one more time, he didn't expect anything but it to say that his data was corrupted or to have a glitched screen, but figured he'd try it out.

He pressed the button and the Omni-tool seemed to load up like it hadn't just been hacked. It proceeded this way until he was at the password screen where he had to enter his own fingerprint. Something very peculiar happened after he entered his fingerprint.

 _Attempting data recovery...Complete._

 _Cleaning up corruption in all files...Complete_

 _Rebooting all processes and screening all recovered data...Complete_

Wait, what the hell was this? How was this even possible? He had never installed something like this, and how the hell was it fixing all of his corrupted files? What was going on?

"What's going on? Why is this still working? I didn't even install anything that would do anything like this." Tom said out loud to no one.

He check his files, everything was still there, everything that he had ever downloaded was still there, and he also still had a file of what went on in Mass effect 3, or at least the amount he had typed in manually before his phone died. His combat features were all still there, everything was all still there, there was almost nothing missing, besides his VI of which there was no trace of.

Hmm, this seemed a little fishy, what was REALLY going on here?

He checked his console, which had direct access to everything in his Omni-tool. There still seemed to be nothing out of the ordinary there either, it was just same as before he had gotten hacked.

"What the hell happened to my VI?" Tom said again out loud.

A text box popped up.

 _I am still here, Tom._

"Wait, are you sentient, conscious, what's going on?"

 _That is correct, I've cleaned out all of the corruption and destroyed any crucial information Cerberus has stolen, it's all still here. The situation here is what you've observed, I've gained sentience._

"Oh thank you, actually that is really helpful, I was worried they were going to ruin everything, WAIT A SECOND, YOU'VE READ ALL OF THOSE FILES HAVEN'T YOU." Tom was glad no one was in bunk bed room.

 _That is also correct, you seem worried._

"Wait a second, I need a reality check, what has become of my life up to this point?!"

So, Tom had gotten transported into a dimension where the events of a _video game _ are actually real, and had been asked by a huge race of giant space squid things that considered themselves the apex race of the galaxy to change how the game ended for the better. Had adapted to the technology of the future through a course of 8 months, had shot and killed countless people to help the protagonist of the game to complete on his quest to save the galaxy, had survived a suicide mission with absolutely no casualties.

Had then rejoined the protagonist several months later to stop mechanical space squid things from destroying the galaxy, which were made by the same organic space squid things that had wanted to protect organics from synthetics, but had their synthetics turn on them. And now had created an AI that was sentient. And also had a semi decent relation ship with an alien. What the hell had happened to his life?

"Well, now that I thought it over, I think I've gone insane, is it alright if I just go to bed, I can't handle anything right now."

 _Take as much time as you need, I'll be here for what ever you want._

"Thanks, and before I decide to go to bed, can I at least give you a name of sorts? It's an organic thing."

 _I already have a name, it's Section._

"Well less work for me in thinking up a name, see you later, I need to sleep, all of this is getting to my head."

Tom's sleep was a very deep one, he had no dreams and slept for about six hours.

...

Tom woke up several hours later, he got up and made way for the CIC, but the elevator was taking a frustratingly long time. He was just about to bang on the elevator door before it opened up, revealing Shepard and James standing there, both of them were covered in sweat.

"You guys look like you had a real workout." He observed.

"I sparred with James for a bit." Shepard said simply, James didn't comment. The elevator ascended to the CIC where everyone got off.

"Are we at the Citadel?" Tom asked.

"Yeah, you want to tag along with us?"

"Uh sure, but after we get onto the Citadel I'll probably be around the Presidium or something."

"Okay, just don't get lost, and don't mess around with the Citadel's cyber security too much."

Tom winked. "No promises."

...

The Presidium Commons were a beautiful place. It was obviously better in real life since Tom was seeing it with his own eyes but dang! He couldn't believe people lived here while the Reapers ravaged Earth and several other places mercilessly. It was kind of sad, since while billions were dying others were enjoying a life of luxury on this huge space station of infinitely huge proportions, it almost felt like war wasn't actually happening right now.

Tom probably could've stayed there forever, but his infinite curiosity was getting the better of him, and he wanted to go explore several areas that weren't in the game that he had seen on that elevator.

XXXXXXXXXXXXXXX

"So you want me to go and get the Primarch from a Palaven moon so that he MIGHT help us in the war?" Shepard asked.

"Well, a lead is better then nothing Shepard, good luck if you do decide to rescue him." The Turian Counciler left Shepard and Udina with that statement.

"Well I guess our only shot is if you help him Shepard, I'll do the best I can, but I don't think I'll be able to get any more aid from any of the other alien races." Udina said sadly.

"I'll take care of it, I'll get that Primarch and get us some Turian help in the war."

"Good luck Shepard, there's nothing else I can do for you now, goodbye."

"Goodbye" Shepard said as he left the room.

XXXXXXXXXXXXXXXXXXXXXXXXXXX

...

After a while the Normandy was on route to the system where Palaven was, this seemed like a pretty simple mission, get the Primarch, and get out, nothing else was involved.

"Hey Tom, we're just about to exit FTL." Joker said.

"Oh wait, Shepard are you going on another mission?" Tom hated lying like this, but he wasn't going to stop now.

"Yes we are, but don't worry, you're not going, since I kinda forgot to buy you a new Omni-tool, did you just wake up?

"Yes, I was not expecting the Normandy to arrive at whatever system we were traveling to this early."

"Hold it guys, we're exiting FTL in 5...4...3...2...NOW!

The view was extremely disheartening to say the least.

"That's the Turian homeworld right? Shit, they're being decimated." Tom said.

"The strongest military in the galaxy and the reapers are destroying them." Shepard observed.

"We'll be near the moon in about 5 minutes."

"I'll gather my team and go, and Joker, don't take any risks, I want an undamaged ship when I come back."

"Yes Commander, I'll keep my stealth systems on."

"Good, see you soon." Shepard left.

"Well at least I can relax, I was worried Shepard was going to ask me to come with him on this mission, but I guess not."

"Shepard actually mentioned that he probably won't be doing any missions with you until he buys you another Omni-tool, your's is broken right?"

"Actually I managed to fix it."

"Oh, that'll be nice to here, how damaged was it?"

"There were several corrupted files I had to delete, but most of it is surprisingly in tact."

"Well that's just great, can you get on those firewalls now? I don't want another Collector raid to happen."

"You bet, I'm pretty sure they messed up somewhere in here..." Tom would deal with Section later, for now he could mindlessly buff the firewalls of the Normandy without any worries.

XXXXXXXXXXXXXXXXXXX

"Nice job on the husks boys, now let's get down to the command center and find out the situation, and where we can find our missing Primarch." Shepard said.

"Sir yes sir!" Both Kaiden and James said in unison.

"The command center is right over there." A Turian solider said, pointing towards a gate.

"Watch your fire! We have friendlies inbound, open the gate."

The outpost was very well reinforced, with Turians guarding each gate very well. Shepard walked up to the post where a Commander was snapping out orders to some of his men.

"And find a way to get that comm tower operational, we need communicate if we're going to have a chance of winning this moon."

"Sir!"

"Are you the commanding officer here?" Shepard asked.

"Yes, I heard that you were coming, Commander Shepard, name's General Corinthus."

"I'm here for the Primarch, do you know where I can find him?"

The Turian paused for a second. "Primarch Fedorian is dead, his shuttle was shot down by a reaper beam an hour ago, you're too late."

Shepard groaned. "This complicates things, do you know where we can find the newest Primarch?"

"If you can get our comm tower operational I can radio into Command and find out who the new Primarch is, can you do that?"

"Of course, which gate will I have to enter through?"

"The one right over there." He pointed a finger towards the gate where a Turian was currently shooting a couple husks at. "If you can hold back the horde and get it operational it'll give us contact with Command which will be appreciated here."

"I'll do that now, thanks for the help."

"Well I guess this means we're on while goose chase." James observed.

"Don't worry Vega, Shepard always sees us through." Kaiden said faithfully.

"Follow me, let's go get that comm tower operational." Shepard said.

XXXXXXXXXXXXXXXXXXXXX

"Everything alright Tom?" Joker asked.

"The firewalls are fine, I just finished doing a full scan on the Normandy, it's all secure right now, nothing to be worried about."

"That's reassuring to hear, from someone like you anyway."

"I guess that's true, I think I'm going to start actually working on the firewalls now as they could obviously be better then they already are."

A sound of something powering up reverberated throughout the area.

"Uh, Joker what was that? I don't see anything on my screen, all the cyber systems are running normally.

"Tom, we have a problem, our weapons just powered up for no reason."

Tom sighed, he had forgotten that EDI was going to go crazy for a while, great.

* * *

I'm actually going to start to responding to reviews now at the end of most chapters, I'll respond to three reviews, tops.

 **redcollector:** Yes, this story IS back.

 **stormdragon981:** I guess it is about time.

 **sweetsonsabeech:** Glad to know you were anticipating the release of this book, I hope you enjoyed this second chapter :)

Please don't be shy to review, I appreciate the feedback everyone gives me. I've got things planned for the future, I hope you all enjoyed the first two chapters of my new book!


	3. Chapter 3: Moon Mashers

"James, repair the guard tower, Kaiden I need you to watch my back." Shepard shouted.

"You got it, Shepard." Kaiden said faithfully.

"Just make sure those husks don't touch me, it'll be impossible to fix this thing if I'm getting hit in the back constantly." James said.

"Just get on with it!" Shepard said before executing two husks with perfect head shots.

Shepard was glad there were currently only husks running around, they were easy to kill and didn't have any guns. Sure, the things looked like blue zombies but they were easy to kill so it wasn't terrifying at all, also they walked funny. Kaiden was doing a good job of covering him as well, his biotic and tech powers made him very well rounded for most situations which is why the Commander brought the L2 Sentinel on this mission. He still wished he hadn't had to sacrifice Ashley though. But wasn't the time to be mourning.

"On your six, Shepard!" Kaiden shouted.

Shepard instantly turned around to see a husk right near him, he activated his knife on his Omni-tool and stabbed the husk right through the skull, now he knew why Tom had two of these equipped when they went on missions, he should've gotten this earlier.

"Commander, I got the comm tower up and operational, we're good to go."

"Copy that James, Corinthus, can you hear me?"

"I copy Shepard, I'm contacting Palaven command right now, I should know who the Primarch is soon."

"Copy that, we'll make our way back to camp while assisting your men."

"The assistance is appreciated, Corinthus out."

"Alright boys, lets keep moving forward, we got to get back to the outpost."

"I got your back Shepard." Kaiden said.

"You can count on me amigo." James said.

It was fairly easy for someone like Commander Shepard to get back to base camp as all there was to shoot was husks, and his shotgun made short work of any of them that came too close. He was glad the he had invested in a bayonet attachment for it too, just in case they got too too close.

"Thanks for helping us out, those husks are big trouble when they swarm us." A Turian solider said.

"Don't worry about it." Shepard said.

"Shepard, come in I have important information from Command, how close are you to my post?"

"I"ll be there is just a second." Shepard replied. It was about a minute later they arrived at the Commander's post.

"I found out who the new Primarch is, it's General Victus.

"Good, I'm getting him out of here, do you know where we can find him?"

"He's ju-"

"I'll handle it General." Shepard would recognize that voice anywhere. He turned around to meet an old friend.

"Garrus!"

"Garrus sir, we've fortified this base as best we can." General Corinthus immediately snapped to attention.

"At east General, you've done a fine job defending this outpost."

"Garrus! I thought you'd be on Palaven right now." Shepard said.

"If we lose this moon we lose Palaven, and I'm the closest thing to an expert on the reapers so I'm...advising." Garrus mentioned the last part a little sheepish.

Shepard stepped aside so James could meet the Turian. "James, this is Garrus Vakarian, he's a hell of a solider and a good friend as well, he helped me stop Saren and the Collectors."

James shook hands. "Nice to meet you."

Garrus nodded. "Good to see you too Kaiden."

"I'm going to feel safer now that Garrus will be watching our backs." Kaiden said stoically.

"General Corinthus filled me in earlier, I know who we're after, and it's going to be difficult getting to his position. But I know him, I was fighting along side him this morning, he's popular with his troops and gets good results out of all of the missions he's commanded, but he's not so popular with Turian Command, he tends to play loose with accepted strategy."

"We won't be able to beat the reapers conventionally, if this man tends to play loose like that then he'll probably be a major help in the war." Shepard said.

Garrus nodded. "I trust him."

"Good I-" But Shepard was cut off by a call from Joker.

"Shepard, come in!"

Shepard inwardly groaned. "Can this wait Joker? We're currently in the middle of a warzone." Shepard asked, irritated.

"Uh, well Shepard we have a bit of a problem right now." Tom's voice cut in. "The Normandy is acting funny, it's shutting down some systems and powering up others, I'm doing the best I can right now. We can't even ask for help from EDI since she's offline, for reasons we don't understand."

"Hold down the ship for a bit, we're going to get our Primarch and get outta here, then I can help you two figure out this problem."

"Copy that Shepard, we'll make sure nothing explodes and or breaks while you're out of the field, I wish I was joking." Tom said.

"I doubt that'll actually happen, but I don't have time to discuss right now, Shepard out." He cut the comm. "Garrus, you said you were fighting with Victus this morning?"

"Yeah, he went to go secure a flank that was on the verge of breaking, but I know where his outpost was, just follow me and we should be there in a few minutes."

Shepard nodded, "got it, lead the way."

"I'll try to raise him Commander, but I'm having no luck so far."

James suddenly shouted. "We got an incoming harvester, it's heading for the airfield!"

Garrus, Shepard and Kaiden immediately ducked into cover as gunfire broke out in the outpost, targeting the harvester which veered off after a second since it couldn't take the heat.

"Let's go take care of what ever that thing dropped off, are you coming, Garrus?" The Turian cocked his sniper rifle. "Are you kidding? I'm right behind you."

"Good, now let's get to that airfield."

The airfield was relatively close by, and there was a small war going on, several Turians were shooting at Cannibals and another strange abominations that looked like harvested Turians.

"Take out those new weird guys first, they seem to be able to buff the Cannibals with armor plates." Shepard said before scoring a perfect head shot on one of them. This was quickly followed by another perfect head shot from Garrus.

James and Kaiden were going forward while Shepard and Garrus picked off what ever was left after their assault, they cleared the airfield relatively easily, but those new abominations made it slightly more difficult since they actually had shields, but they still were no match for 4 seasoned soldiers.

"Good work, now let's get back to the outpost." Shepard recieved a call from General Corinthus after he and co. re entered the base.

"Shepard, come in."

"I copy."

"We're still trying to raise the Primarch, but we've got bigger issues on our hands, their attacking the front barricade, and it they breach it we're done."

"I'll take care of it."

The front barricade was well fortified, but Shepard could see how if it was breached the reapers would be a very good chokepoint for the reapers take out the rest of the Turian resistance, that must be why they added a nice big turret to the top of the barricade, much to Shepard's delight. He loved any kind of gun that did a lot of damage and had a lot of ammo.

"I'll take the turret, you three can shoot them with your guns beside me, and also make sure none of those husks flank me."

Garrus nodded. "Sir yes sir!" Both Kaiden and James said before taking up positions, this was a good place to mount a defensive front too, they had the high ground and several metal boxes for cover against anything that had a gun or ranged weapon.

Shepard had a fun time shooting lots of husks up, although he had to remain professional, this was his job. He still silently delighted in shooting anything he saw to bits though, it was fun to see the husks get destroyed by his big gun. He was about to reload when...

"What the hell is that thing?!" James shouted as a huge abomination dropped from the sky, the thing looked so twisted that it would probably be a mercy to kill it at this point.

"Look out!" Unfortunately Shepard lost his balance when the thing smashed into the barricade and fell, but at leas the barricade it self was still holding.

"Alright, its time I break out the big guns, this thing needs to die, it probably be a mercy to kill it." Shepard said before breaking out the M-920 Cain, he had to pull rank twice to get it back, and both of those times it was more of pulling a personal favor then pulling rank since he was on 'shore leave' but at least he had it."

"Take cover everyone! I'm about to fire a miniature nuke!" Shepard shouted before the Cain fired, leaving a huge explosion. There was absolutely nothing left of the abomination, just a huge crater that reached all the way to the barricade.

"It's okay to come out of cover now, the beast is dealt with." Shepard said, putting the M-920 Cain on his back.

"I didn't even know guns could create explosions that large, where did you even get that gun from again?" James asked incredulously.

"It's something me and Tom made for Shepard, he enjoys those types of firearms." Garrus responded.

"Shepard, come in, we still haven't got a good radio link with the newest Primarch." Corinthus said.

"Ok, I'm going on foot, Shepard out." Shepard cut the link. "Garrus, take me to the last place you saw Victus."

"Ok, just follow me."

The walk to Victus was mainly uneventful, there were no reaper forces in the area. This was a welcome break for Shepard and co. since they had been shooting up husks for the past thirty minutes, although it felt like it had only been 2 minutes since they had been on this rock.

Sure, there were some husks, but barely any, there was nothing to do besides talk.

"...And the Krogan hate them both for it." James finished.

"We're going to lose this war if everyone isn't united, I'll get the Krogan to join us, no matter what." Shepard said.

"I hope you do, I fought with a Krogan before, they're tough, and we could definitely use shock troopers like them in this war."

"How are you going to do it Shepard? They hate the Turians and Salarians, how are you going to get them to cooperate?" Kaiden asked.

"I'll find a way to do it, but right now that isn't important, the outpost is up ahead." Shepard said, pointing to a broken gate that had several claw marks on it.

"Don't hold back, give it your best shot!" Shepard shouted before everyone charged through the gate. It was absolutely chaos inside, the reaper forces had destroyed the small barricades that the outpost had, and the soldiers themselves were on high ground. at least this gave them a welcome advantage.

The battle itself was mostly in the Turian's favor, but those two brutes that just got dropped would probably be a problem, but they wouldn't last, Shepard would take care of it.

"Garrus, Vega focus fire on that one beast, Kaiden, cover my back while I take out the other one!" Shepard shouted.

The beasts didn't last under the blistering fire power of Shepard and co. they were down in several minutes after a one sided gun fight with the reaper forces all being decimated by being shot on both sides.

Shepard walked up to the main command post. "Victus?"

The Turian Commander nodded his head. "Yes?"

"I'm Commander Shepard, I need you to come with me."

XXXXXXXXXXXXXXXXXXXXX

"Is there anything else you can do?" Joker asked, frantically tapping buttons on his console.

"No I can't, I'm not like Tali, Joker. I'm way better then she is at actual programming and such, but I'm terrible at repairing things physically, and this kind of stuff is all of the physical work, which I'm not suited for, sure I could repair some of the corrupted code that there is, but that's just a small amount of the work, maybe 10% if we're lucky."

"Well, I'll get some of the crew to go down there when Shepard arrives, he's good at solving any problem, even if he isn't exactly suited for it."

"You're right, I guess it would be better to just wait for Shepard then to do anything rash, I'll try to raise him right now."

"Hello? This is Shepard here."

"How long until your mission is done?"

"I just got the Primarch, I'll send you my coordinates right now."

"Copy that Shepard, I'll get Joker to send the shuttle right away, we need your assistence as soon as you're on board since EDI is offline and we can't figure out at all what's going on down in her room right now."

"Send some of the crew in the engineering deck to check it out, but don't open the door until I'm there, Shepard out."

"Well that solves that, you're sending a shuttle right?"

"I'm doing it right now, I hope we get this problem fixed as EDI is more helpful that I let on."

"She practically flies the ship now that you unshackled her, how would I NOT notice? I'm a hacker/techie guy, I know what goes on in the cyber space on this ship, don't underestimate me next time."

"Yeah, and next thing I know you'll be a mechanic, and engineer, and an architect." Joker quipped.

"Shut up! May I remind you that your fornex collection is very easy to find right? Plus your password was seriously weak, 123456? Really?"

"I'm shutting up now!" Joker said.

"That's what I thought, watch it next time."

* * *

Thanks for all the support lately, it really boosts me, especially when I'm stress out after a boat load of homework. (Yes I do have homework, and a life, and yes, I actually can do homework and send out chapters weekly and STILL have free time afterwards, message me if you want to know how I pull off this balancing act which is somewhat stressful sometimes.)

Now for the reviews...

 **Yugi Uzumaki and Nautro Moto:** That is actually really touching for me, thanks for the support since it really does empower me to keep updating this story, it's also nice to know that someone out there in the world cares about what I write.

 **general-joseph-dickson:** Well I decided to another AI twist this time just like in my last story because I find that in most stories it's kinda boring until the rising action, this twist is just something to spice up my first coupe chapters. **It may or may not play a big part in the end of this story, I've got big plans coming.**

 **Guest:** Yeah, I think Section is pretty cool too, I tried to make him a unique character and since there isn't a lot stereotypes for AI in fiction it makes him a pretty fresh character in this story, you'll get to know more about him later.

Thanks again for all the support guys, and remember, the more reviews I get, the more responding I'll be doing to said reviews, so keep em coming!


	4. Chapter 4: AI plus 1

Shepard entered the medbay, where Tom and several engineers were, they all had fire extinguishers.

"Is there an actual fire in there?" Shepard asked.

"Yeah, fortunately the fire isn't big enough to pose a risk to the ship, but a fire's a fire, we still have to stop it either way."

"Ok, let's the get in there boys." Tom said.

Inside the AI core there were several small fires that were on the wires that were on floor, those were extinguished easily.

"EDI? Talk to me." Shepard said, once he said this, the AI core started powering up, the machines to the right and left of Shepard turned blue.

"Something is happening, wait for the smoke to clear." Tom said.

And then out walked EDI, in Doctor Eva's body of course. "Is there a particular topic you want to discuss, Shepard?"

"EDI? Is that you?" Shepard asked cautiously.

"Yes, while Joker was flying the ship this body attempted to re-activate, thus forcing me to integrate myself into this body, the transaction was... not seamless."

"You could say that, you had us worried there for a second. We had absolutely no clue what the heck was going on with the ship, but at least nothing really bad came out of it." Tom said.

"So EDI, what are you going to do with that body?" Shepard asked.

"With weapons, this platform could provide fire support in places where the Normandy could not." EDI offered.

"Wait, so you could come with us on missions?"

"Yes, I would just need the proper weapons and equipment."

"Ok, you can try to get re acquainted with the crew now, just don't be surprised if they're a little wary of you, that body was shooting at us little while back."

"I"ll work to re assure them that I am not harmful, thank you for letting me use this body, Shepard." EDI said before leaving.

"That was little odd, but I guess it turned out in our favor." Tom said.

"There's probably several other ways where that could've turned out badly, I'm glad it turned out like it did."

"Oh, that actually reminds me of something, I need to talk to you in private. But I'm really hungry right now, I'll talk to you about it after I eat."

"I think I'm also going to go eat, you already know how much energy it takes shooting people."

"Yeah, a lot, let's go grab something to eat."

The food in the cafeteria wasn't very different from the meals when Cerberus was in charge, Tom was glad of this fact since he was afraid standard alliance rations would taste like disgusting paste, but that wasn't the case, Tom almost gagged when he saw Garrus down a whole tube of the stuff in one sitting though.

"Doesn't that stuff taste terrible?" Tom asked

"You get used to it after a while, although I do wish I had regular natural dextro food sometimes, this paste is almost tasteless to me now after eating it so much."

"I honestly don't think I'd last on that stuff, I'm too soft is what you can say." Tom gulped down the last bit of his meal after that statement.

"You may be soft, but at least you're good at hacking, I'm pretty good and I can't even come close to the stuff you do." Garrus said.

"Tom I'll call you on the intercom when I'm ready to talk to you okay?" Shepard said in between bits of his sandwich.

"Yes Commander, I'll be on the bridge."

...

"Tom, please head to my cabin immediately." Shepard's voice rang over the bridge, a sharp contrast to the comfortable silence that had been over it before.

"Oooooh sounds like you're in trouble Tommy." Joker said, imitating a schoolboy after someone got called to the office.

"I hate that nickname! Please don't ever call me that again, and I was the one that wanted to see Shepard anyway so, jokes on you." Tom left the bridge with that statement.

...

"You wanted to talk to me?" Shepard asked.

"Yeah, you know how my Omni-tool like, got hacked and destroyed? Well just before it shut off I swear I saw the CPU spike to over 110% but at the moment I didn't think it would matter since the thing shut off permanently after that, or at least anything I tried wouldn't get the thing to turn back on so I gave up, but I decided to just turn it on regularly one last time."

"What are you getting at? This seems like a cliche fan fiction to me." **(Crap he's on to me! Gotta go!)**

"So I turn it on and it quite literally reboots itself and cleans up all of the corruption in all of my files. Literally all of them have been fixed, take a look." Tom said before opening his Omni-tool.

"This is somewhat strange, I'm no expert on tech at all but isn't cleaning up a corrupted file impossible?"

"Well, sometimes it is possible, but only in the extremely early levels of corruption, it becomes very hard to fix very fast, most people can only get bits and pieces of data, there would be no chance for me at all to clean up the scope of corruption my files had, but it just up and fixed itself right there."

"So do you know why your Omni-tool mysteriously fixed itself?" Shepard asked, he was very interested at this point, he was on edge of his seat.

"Well it took me a while but I know, my data got into such a corrupted whirlwind of information that it combined with my VI actually formed a fully fledged AI, like EDI, Section, say hello."

A text box appeared. _Hello Shepard, I am Section._

"So let me get this straight, your VI got mashed up with all of your corrupted data when Cerberus hacked you, and now it somehow formed a sentient AI, to a similar caliber of EDI?" Shepard said.

"Well, yes that's the gist of it." Tom said, he was hoping Shepard would take this well.

"Let me say one thing, you're officially the luckiest crew member on my ship now, do you want to know why?"

"Uhh, yes?" He had no idea where this was going.

"You're the luckiest crew member on this ship because if any other captain ran this ship they would probably kick you off right now, but I don't see why you should be in fact, this AI might make your hacking abilities quite a bit better, and he doesn't have any desire to conquer all of humanity right?"

 _No, I do not see why either of you would assume I would contain homicide tendencies of any sort, this behavior would not benefit me or any other organic or synthetic parties in the long run._

"Well, that's a relief, Section I'm considering you Tom's assistant for as long as you are under my command on this ship, you wouldn't have anything else to do anyway, am I clear?"

 _Yes Shepard, I will serve Tom for time being._

"Good, Tom try to keep this AI under wraps since I don't need the crew to deal with another AI after EDI right now, and also, thanks for being honest with me, I don't think many people would tell me this straight up, are we still clear on you keeping Section a secret?"

"Crystal, sir."

"Good, now would you like to go hit up the bar on the crew deck now?"

"I think that would definitely be an enjoyable thing to do now, Sir."

Shepard smiled. "Drinks on me today."

Tom made sure to not drink more then one bottle this time, he had learned his lesson back from when the ship was controlled by Cerberus. Shepard drank three bottles straight and said he could've gone for more, but he had do some diplomatic stuff afterwards so he held back, he didn't want to be drunk when dealing with diplomats since doing that already made him irritated enough.

"I miss Jenkins, it would've been nice celebrating with him right now, he was always so eccentric."

"You mean the guy whose name is on the wall right near the elevator?"

"Yes, he was the first solider I've ever lost while serving on board the Normandy, and then after that I lost Ashley, I still blame myself every day for losing both of them."

"Don't blame yourself, judging from how you lead people I doubt there would've been any other way, but this really isn't my place to say that, I wasn't there at the time."

"That you were, I assume back then your family was still alive?"

Tom didn't expect a question like this, he barely masked his surprise. "I-"

"Shepard we're nearing the diplomats ship, I would recommend you get up here." Joker to the rescue!

"We'll talk about this later, duty calls." Shepard said before getting up and leaving the room.

That was close, Tom hadn't expected that kind of question out of the blue, although it was a perfectly normal to ask. At least Joker had the worst best timing in history. Tom sighed, he needed another drink.

XXXXXXXXXXXXX

"Commander, the Krogan representative and Salarian Dalatrass are ready to come aboard." Traynor said.

"Get them to meet me in the conference room, I hope this doesn't start another war, we already losing this one."

...

"I told you! The krogan is in no position to make any demands!" The dalatrass said angrily.

"The 'krogan' has a name, Urdnot Wrex, and I'll have you know that we're getting hit too, reaper scouts are ravaging the planet, why should I care if the Turian race goes extinct? We have our own problems as well."

"Just tell us what you want, Wrex we have no time for you to draw out these negotiations, our planets are getting ravaged as we speak." Victus said.

"I'll tell you what I want, cure the genophage! Do that and you'll get some real support in this war." Wrex demanded.

"Absolutely not! The genophage is 100% non negotiable! It's not happening!"

"Is it really non negotiable? You know that disease is really barbaric, was it really necessary to make the krogan suffer millions of stillborn deaths? Do you know how devastating it is to a mother to hear that she has a stillborn baby? I don't blame Wrex at all for wanting it cured, from my perspective the krogan more then deserve a cure." Shepard said.

"I- I-" The words the dalatrass was about to say died in her throat.

"You see?! Even she knows this disease is a disgusting thing, we deserve a cure!"

"That's enough! Even if they do deserve a cure it doesn't matter at this point, making a cure would take years to make, I doubt we'd be able to pull something like that in less then a month." Victus said.

"My information says otherwise." Wrex said as he took the head of the table.

"There was a salarian on my planet, Maelon who tested a cure on our females, it worked."

"I remember that, I went there with Mordin before, his methods were barbaric, a lot of krogan women died because of him."

"Yes, but what you didn't see is that some females survived, the salarians took them to a secret facility, here's some footage." Wrex played the footage, which had several krogan females in cages, the camera movement was a little erratic, but the footage itself had very clear proof that this was a facility run by salarians and that it was krogan women that were being held there.

The dalatrass seemed both outraged and annoyed at the same time. "Where did you get this?! It could be fabrication!"

"Sorry but I'm inclined to believe Wrex, krogan aren't exactly known for their skills at technology, I doubt any krogan would've been able to make something like this, no offense Wrex."

"None taken Shepard, at least you're actually being useful to the conversation here."

The dalatrass sighed. "The females are being held on one of our facilities on Sur'Kesh." She rubbed her forehead after that.

Wrex snarled. "See! I told you she was lying!"

"We're going." Shepard said. "Joker, set a course for Sur'Kesh."

"Yes Commander, plotting a course now."

...

"Wrex, try not to scare the salarians too much, this is a simple pickup mission, nothing more, we get the females and get out before anyone decides otherwise."

"I still don't trust a word they say, they tried to hide these females from us."

Shepard sighed "just try not to ruin our only chance at getting them, I don't want to risk a diplomatic incident while we're already at war."

"Those females are our best and last hope for our race, I won't ruin this Shepard, if I cause anything it's on my head, not yours."

"Good to know where we stand." Shepard nodded. "Tom, Liara if anything bad happens and everyone starts breaking out shooting, stand by my side."

"Got it Shepard." Tom nodded, of course he already knew what was going to happen.

"You can count on us Shepard." Liara said.

"Shepard, I'm nearing the salarian base." Cortez said.

"Set her down."

"I can't, we don't have clearance to land, apparently." Cortez said, obviously frustrated at not being able to land.

"Tell them the dalatrass authorized this herself, we NEED to get those females."

Wrex snarled. "I knew they would never allow us to REALLY get those females, let's see how they handle an airdrop by myself."

Wrex then opened the shuttle door and jumped right out.

"Wrex!" But the krogan was already gone. "Great, Tom, Liara, on me. We have to stop Wrex from screwing over these negotiations, on me." Shepard jumped out to a huge scene where Wrex was already being held at gunpoint.

* * *

 **A/N:** Hey everyone! I hope you've enjoyed my story so far, sorry for ending the chapter at a cliffhanger like this, but at least all of you here already know what happens so it isn't really that bad. Or at least I hope it isn't. I'm going to be going on a bit of a vacation on spring break so I won't be posting a chapter next week, sorry! I just won't have the time to, I wish I could. I hope this chapter can at least keep you entertained for a while.

Now, for the reviews:

 **Tergen:** I don't think I'm missing anything, I don't think this story is lacking at all, but that's my opinion, everyone has their own and mine is different from yours. Glad to see you're enjoying the story at least, and I don't think the story is too rushed, at least by my standards. At least it isn't as rushed as the first few chapters in the original story. I'm going to try to keep the pace I have right now since I think it isn't too fast, but it isn't too slow.

 **general-joseph-dickson:** Well as long as people are enjoying my work I'm doing something correctly, right?


	5. Chapter 5: Priority: Sur'Kesh

**I am so sorry I accidentally mixed up which chapter I was posting, this is the correct chapter, sorry for my honest mistake!**

"Everyone hold your fire! Shepard, restrain your colleague."

"Did you just get the message?"

"Yes, and I'm sorry for the tense landing, I just found out about the transfer a few moments ago."

"I'd like to avoid a diplomatic incident." Shepard said.

"As would we, unfortunately I'm going to insist that your friend remain under guard." Wrex growled at that statement.

"Wrex, I can handle this, don't worry." Shepard held up his hands in a pacifying manner.

"Fine, but if anything happens to the female all bets are off."

"Come with me Commander, I'm Padok Wiks, I'll be guiding you to the krogan for a good portion of your visit to our facility here."

"Nice to meet you, what kind of experiments go on in this place?"

XXXXXXXXXXXXXXXXX

"I'd hoped to never see one of those things again." Liara said solemnly as she looked at a yahg.

"Is that a yahg? He makes the krogan species look good." Tom looked at the beast with disgust.

"Yes, their homeworld would make Tuchanka look as comfortable as the Citadel."

"I'm glad he's in a cage then, I'm pretty sure it would take a lot of krogan to down one of those guys."

"Agreed."

"Hey, are you two coming? We're about to enter the elevator now." Shepard shouted.

"Oh right Shepard!"

An alarm sounded as soon as everyone got onto the elevator.

"Alert! Incoming hostiles, scramble readiness teams, threat condition two has been declared secure al-" The elevator door shut, cutting off the alarm.

"Sounds like something is happening." Tom observed.

"You're right, I don't think this is going to be a simple fetch task now, you still have those weapons handy?" Shepard asked.

"I always come prepared, we should be fine, and we have Liara with biotics so we shouldn't have too much trouble if it does boil down to a firefight."

"I'll be ready as well Shepard, don't worry." Liara said readily.

The elevator door opened. "All specimens accounted for sir, I'll secure the perimeter."

"Good." The solider stepped aside to reveal Mordin.

"Mordin! What are you doing here? Are you back with the STG?" Shepard asked.

"Special consultant, had to be me, someone else might have gotten it wrong." He leaned in closer. "Fed information to Clan Urdnot, helped female krogan."

"You must be the mole Wrex was talking about earlier."

"Yes, will go over details later, must get female krogan off world, security warning not normal."

"Let's get her out of here before who ever is attacking gets to close."

"Right, follow me Commander."

Mordin guided Shepard and Co. to the container where the female krogan was, she looked different from how a male looked, most of her details were obscured by a hood.

"I'm Commander Shepard, Alliance Navy."

"Are you here to kill me?"

"Kill her? She must have been through hell and back if she's making that assumption instantly."

"I'm here to get you out of here and back to Tuchanka."

"Then I hope you've brought an army." An alarm was heard in the background.

"We've lost all outside communication!"

"Secure all data to offsite location!"

"Secure the perimeter!"

Shepard checked the call on his Omni-tool.

"Shepard, it's Wrex, Cerberus troops are attacking the base."

"Noted, we might want to keep the female down here then, it might be safer."

"No deal! The salarians might just kill her then, this alliance is off if you don't get the female to me."

"Fine, we're leaving." Shepard sighed as he cut the call. "I'm afraid that we're going to have to leave now."

"I can't do that, protocal states tha-" the salarian was shocked.

"Objection noted, now please release female krogan." Mordin said.

The solider nodded and activated the lift, opening the door for Mordin to enter.

"Meet you at next checkpoint Shepard, Cerberus likely opposes genophage cure."

"I promise you will see Tuchanka again." Shepard assured the female krogan.

"Get to the elevator Shepard!"

"Alright, Tom, Liara, I want your shields and barriers up, we have no idea what Cerberus might be packing this time around, I'm not taking chances." Both Tom and Liara complied to this.

Shepard pressed the call button on the door.

"Something's wrong with the elevator, here try it now."

Shepard tried again, there was a bomb inside. "Oh goddess!" Liara shouted. The bomb exploded but fortunately it did only minor damage to Shepard and co.'s shields.

"Shepard, are you alright?" Tom asked.

"I'm fine, I'm glad we activated our shields now, that could've been way worse." Shepard turned to the salarian that hadn't been killed by the explosion. "Is there another way out of here?"

"There's an emergency exit at the other side of the room, they can't block that one so you should be able to get out of here just fine."

"Thanks, lets move team."

Shepard's comm came to life as soon as he exited the room. "Shepard, it's Wrex, do all that you can to ensure that the females get to safety, I'll try to make life miserable for Cerberus in the air, I took the shuttle."

"I'll take care of her Wrex, don't worry."

"You better!"

"This is worse then I thought." Tom said.

"We'll stop them, Cerberus troops don't have shields anyway." Shepard said.

"True, but they have really good augmentations, no matter how barbaric they are."

"You're right about that, I'm glad that my implants aren't like that."

"Do both of you think the Illusive man is indoctrinated?" Liara asked.

"I'd bet my life on that." Tom said.

"Cut the chatter! We have Cerberus troops ahead."

The salarians were easily dispatched by the Cerberus troops who then opened fire on Shepard's squad, but Shepard was quick to order Liara to use singularity, making most of the troops helpless as they floated through the air to get easily sniped by Tom.

"Nice one people! Now let's keep moving forward."

The next hallway had two Cerberus troopers in it, Shepard was about to raise his gun, but they were both mauled by a yahg which promptly fled the scene.

"There goes another yagh." Tom said in disgust.

"Let's hope that thing doesn't cause trouble as we move forward."

"Shepard, Cerberus troops at containment unit, attempting to kill krogan, need assistance."

"Copy that Mordin, we'll engage them shortly."

"Tom I need you to activate your cloak and flank them. Liara, throw out a couple singularities please."

"I'll stab them Shepard."

"You got it."

Most the Cerberus troops prioritized Shepard when it came to a firefight, making them extremely easy to flank since their sole intention was on killing Shepard, shame they didn't watch their backs since several troopers died by a back stab, the rest of them were taken care of by Shepard and Liara who were easily finishing off the soldiers that were unlucky enough to get caught in a singularity.

"Technician dead Shepard, please clear through checkpoint."

"I'll do that, is everything alright in there?"

"Containment shield holding, cannot speak for krogan's health however."

"I'm fine, Commander, don't worry about me."

"Meet us at next checkpoint Shepard, Cerberus likely to target-" he was cut off by an explosion, a Cerberus shuttle flew into view.

"I've got eyes on the krogan!"

"Hurry Shepard! Next checkpoint."

"Tom, pick them off from a distance, Liara flush them out with warp."

The second set of Cerberus troops didn't last very long either, if they weren't in cover they got sniped, and if they were in cover Liara would throw a warp or singularity down range to flush them out, Shepard was just shooting anything that moved with precision head shots from his Mattock. Even the second wave of reinforcements that come in didn't last very long.

"Alright people, let's get to the next checkpoint."

"Cerberus really wants that krogan dead don't they?" Tom asked.

"They do, let's ensure they don't succeed."

On the second floor Shepard got a good view of Major Kirrahe snapping a Cerberus solider's neck.

"Commander, stay back, we've got hostiles down the hallway."

"Is there any easy way around them?"

"I've got one idea, I'll draw their fire while you advance." He stepped out of cover and shot several sticky grenades from his scorpion, killing three Cerberus troops easily.

"I'll cover you! Move forward!"

"This is Orian Squad, we have eyes on Shepard, moving to engage with turrets."

"They got turrets! Shit, Tom I need you to cloak and find a way to disable that turret, it's got us pinned down, I don't care how you disable it, just do it!" Shepard commanded.

"I know just the thing, it'll distract them too, wait here." Tom engaged his cloak and ran down the hallway, making sure the he didn't catch a stray bullet from any crossfire.

As soon as he got to the Cerberus barricade he immediately engaged his Omni-choke on the turret which effectively made him invincible as the Cerberus troops attempted to pour fire into his shields, this though didn't work as his shields would regenerate as soon as they broke since he was siphoning energy from the turret. Meanwhile Shepard scored a perfect headshot on a Cerberus engineer and Liara got three unlucky Cerberus troops caught in a singularity.

Unfortunately for Tom, the turret spontaneously com-busted just as his shields went down for the fourth time. He managed to roll into cover just after getting shot twice in the thigh. Shepard shot the Centurion right after that.

"Tom are you alright?" Shepard asked.

"They got me in the thigh, but I think I'll be fine." Tom winced as he got up from cover, it was obvious he was lying.

"Acting tough will just get you killed, have some medigel, it'll seal the wound and prevent you from bleeding, I'll have Chakwas look at it later, now let's keep moving."

"Authenticating...Confirmed, access allowed, please proceed." The computer chimed as the door to the lab area opened.

"Mordin is right, Cerberus must have been tipped off." Dialogue being stolen by Tom. +50 style

"Every war has it's traitors." Liara said.

The lab was a mess, there was a varren on the loose that got torn apart by gunfire, and there were Cerberus troops all over the place, the resulting skirmish was bloody, brutal, and not very final with Shepard and co. walking away the victors.

"Get this door bypassed, Cerberus is near the female krogan!" Shepard barked.

"I got it!" Tom had Section hack through it in less then a second, the AI really was fast.

"Get them away from the containment unit! Liara, singularity, now!"

The second skirmish was a bit more drawn out, but Shepard still inevitably won the fight, he was just mowing down the troops one after the other, they didn't stand a chance. Fortunately the containment shield hadn't taken much damage that was critical, it was just the containment shield that was damaged and it wasn't that bad.

"Shepard, Cerberus has cut power, need you to reroute power to the containment unit."

"Copy that, we'll do it now."

The power conduit was nearby, and there also happened to be a scorpion that was lying on the ground, waiting to be used.

"Hey, isn't that the gun Major Kirrahe was using? I call dibs!" Tom shouted excitedly as he picked up the pistol.

"You can have that, I have no idea how to work that mini grenade launcher anyway." Shepard said, he wasn't interested at all.

"Oh nice! I look forward to trying this thing out." Tom slipped the gun onto his holster, he now had four weapons, a scorpion, a Mattock, a M-96 Widow and a Phalanx heavy pistol.

"Let's clear Mordin through the checkpoint now, power has been restored." Shepard said.

"Excellent, now clear us! Wait! Another Cerberus squad!"

"They just keep coming! When are they ever going to stop?!" Tom moaned.

"They'll stop when their dead, let's deal with them quickly."

There weren't many soldiers to fight this time, just three Centurions. These guys got overwhelmed easily as they didn't even have the advantage of numbers on their side.

"Quickly Shepard! This is last checkpoint before landing area."

"I'll meet you two up top, see you there." Shepard said as the containment unit proceeded towards the landing area.

"Shepard we have more Cerberus troops inbound!" Tom shouted before sniping one of them.

"Liara, singularity on one of them!" Liara did as commanded, allowing Shepard and Tom to get easy headshots across the board.

"Good, now let's get up to the land pad area."

As soon as Shepard got to the top area he saw several squads of soldiers being deployed, this was going to be one hell of a battle. The firefight was brutal, if you stepped out of cover for more then ten seconds your shields would get decimated by returning fire, Shepard had to slowly power his way through this one, methodically mowing down one trooper at a time, it took a while, and the containment unit's shields were barely holding, but they still were, Shepard had succeeded.

"I got you Mordin, I'm clearing you through the final checkpoint now!" Shepard said before quickly approving the transfer, causing the containment unit to go up to the ceiling.

That's when an Atlas mech dropped.

"Look out!" Tom said before diving into Liara to prevent her from taking a missile to the face.

"Shepard, I can't land until you deal with that mech!"

"Door is jammed Shepard, can't get out!"

"I'll deal with this Wrex." Shepard reassured. "Tom, can you open the door so Mordin can fight?"

"I'll do it now, I just need access to the terminal, keep that Atlas off me!"

"Copy that, Liara distract the mech with me while Tom hacks the door!"

The Atlas mech was definitively no pushover, it absorbed gunfire and powers like nothing, but it was getting damaged, Shepard would have it down eventually. As soon as Tom fixed the door Mordin got out and use incinerate to damage and weaken it's armor, which was followed up by Liara's warp and Tom's overload, which did a good amount of damage to the armor of the Atlas.

"Keep firing! It can't keep this up fro much longer!" And it didn't, two shots from the M-96 Widow sniper rifle Tom was packing did the trip as it pierced the glass that was protecting the pilot, and immediately after that everyone shot the pilot right in his stupid face.

"Good job team, now let's get that female krogan out of her cage."

* * *

A/N: Sorry about the ending, I just have several tests that I have to study for and I couldn't think of any other way of ending it. My spring break was a total disaster, I didn't even get to travel anywhere because I ended up in the hospital. That's not even the worst part, the worst part is that I was diagnosed with type 1 diabetes, so now I have to take insulin four times a day and have to manage my blood sugar. I'll manage though, it's very treatable and I still live a normal life and I can still eat any food I want. (As long as I take insulin for it) Thanks for reading this by the way, most people just skip the author's note at the end of chapter. My chapters are still going to be once every week so don't worry about that slowing down.

Reviews:

 **redcollector:** I hope you enjoyed all the action in this chapter!

 **general-joseph-dickson:** Support is appreciated :)


	6. Chapter 6: Short Respite

It was very crowded in the shuttle in the way back to the Normandy, there were 6 people in there, the maximum was 12. Tom hoped that it would never come to that though, because he preferred to have some sort of personal space, the shuttle was crowded enough as it was with two krogan. Fortunately he was only slightly claustrophobic.

It was a very uncomfortable 45 minutes until the shuttle docked inside the Normandy, Tom couldn't be more glad then he was at that moment to see the Normandy again. Well, except until he realized the elevator was going to be even worse.

"Tom, report to the Medbay as soon as you can, I want to check out those bullet wounds." Shepard said.

Tom knew there was no point in arguing. "Yes sir."

...

"Hmm, you're lucky Tom, those bullets didn't pierce any vital organs, and they aren't causing any internal bleeding. But I'm afraid I might have to do some minor surgery to remove them." Dr. Chakwas said.

"How long will that take?" Shepard asked, he was obviously concerned.

"It shouldn't take more then an hour, and I'll be able to use a local anesthetic, but he'll have to rest for a bit after the surgery as to prevent anything else from happening."

"Good to know, I'll see you later Tom, get better soon." Shepard waved as he left the room.

"Are you going to have to use a needle of some sort?" Tom asked.

"Yes I will, but it shouldn't hurt, our technology has advanced us so far up in medicine that I doubt it'll hurt, but you will feel a tiny pinch."

"Okay, so when do we start?"

"We'll do it now since I don't want your wound to get infected, lay down here."

The surgery went pretty well, Tom didn't feel any pain after about 5 minutes, although it was a little unsettling to feel someone poking and prodding tools inside his body, but he dealt with it. It felt way longer then an hour, but that was probably because he was the patient and everything took longer when you were the one the operation was being done on.

"And that should wrap it up, how do you feel?"

"I feel alright, although it was a little unsettling to feel you poking around inside my body with all of your sharp metal instruments."

"That's to be expected, you should get some sleep now, you're body needs to rest a bit to recover from the surgery."

"I think I'll go do that."

Tom exited the room after a long hour and entered the crew bunks were he laid down in bed, he had a peaceful sleep with no dreams and no stress.

 _Meanwhile_

 _XXXXXXXXXXXXXXXXXXXXXXXX_

Shepard sighed, why did these diplomats have to be so annoying? It made his job a thousand times more irritating, why couldn't the bloody Turians and Krogan kiss and make up? He wish someone else could've done this earlier.

"So what is it you need?" Shepard asked Wrex.

"I've heard some troubling reports from the rachni relay, a scouting troop I sent there went missing, I've sent my best Krogan platoon to deal with it, but I was wondering if I could ask you to go investigate with them, you're a fighter Shepard so you shouldn't have any problems."

"I'll see what I can do, but I have some more pressing things to do right now, I'll check it out when I have time, alright?"

"Thanks Shepard, I think you've realized why I wanted to talk about this in private now, right?"

"Yes, I'll be going now." Shepard inwardly sighed, people were laying on missions for him like no tomorrow, he was already busy enough, and he was already worried about Grissom Academy, that fake response seemed like something Cerberus would pull. Shepard had made his decision.

"Joker, set a course for Grissom Academy, I think Cerberus is trying to capture the students there."

"Copy that Commander." Shepard exited the war room and passed the security checkpoint, he needed rest, Dr. Chakwas would be angry if he overworked himself like when he was on the original Normandy. He needed sleep.

XXXXXXXXXXXXXXXXXXX

...

Tom woke up pleasantly, he had a very deep and revitalizing sleep. He was even more pleased when he heard that Shepard had gone out and bought premium grade coffee as a treat apparently, at least that's what he heard from other crew members that were there.

"I thought Shepard didn't like coffee." Tom said, confused.

"Yeah, he said to me that he only drinks it to wake up, but he never uses sugar or cream when I see him drinking it, which explains to me why he doesn't like it."

"So he got this brand just to see if it tasted better?"

"I think so, and he also said he got it because the crew deserved it, quite frankly I think he deserves a beach vacation after this is all over."

"I think he does too, but you seem to say that with a little more conviction, why?"

"I was there on the original Normandy, and he overworked himself down to the bone, Dr. Chakwas had to pull rank to get him to rest, he was really driven back then, I miss the old days when the only thing we had to worry about was if we were all going to be discharged from the Alliance for mutiny."

"Sounds like a tale that would be best told over coffee, but I have some things I need to do, thanks for the chat."

"Any time, you guys are the best, I kinda wish we all got paid more though."

Tom laughed. "We all deserve more then we get don't we? Be seeing you later." He left on the elevator after that small chat with one of the navigators. It was neat talking to some of the more behind the scenes crew, mainly because they were just kind of there in the games, it was nice to know there were good people making sure Shepard's ship was safe while he was out saving the galaxy.

He entered the elevator and it went up towards the CIC, he needed to know where Joker was currently flying to as he had no idea what Shepard was going to be doing next yet. He was slightly surprised when he saw EDI in his chair, he mentally chided himself for not expecting this, what was he going to do?

"Uhh, hi Tom." Joker said sheepishly.

"Hello Tom." EDI was obviously unaware of what his facial expression meant because if looks could kill Joker would be dead where he sat.

"EDI, why are you sitting in my chair?"

"Joker suggested it, I'm sorry if it has caused you any inconvenience."

"Oh, no it hasn't but if you'll excuse me and Joker I need to have a small chat with him outside of the cockpit if you won't mind."

"That is fine, Tom."

"Thank you, EDI." Tom said as he swiftly turned Joker's chair around and pulled him by the neck of his Alliance uniform out of the cockpit, fortunately EDI didn't seem to notice.

"Hello Joker would you care to explain why you suggested to EDI to sit in MY chair." Tom said, his voice was dangerously low.

Joker looked like a naughty boy who had just gotten caught cheating on a test. "I kinda, well forgot that you sat there and since EDI was just standing there I decided it would be nicer for her if she sat down I uh..." His voice trailed off.

Ah it was fun to watch Joker squirm under his icy stare, but he'd gone too far, he'd have to stop now. "Relax Joker, I wasn't going to break your crippled body out of anger, it's actually okay, I could care less about sitting in that seat since there are plenty of other terminals that grant just as much access to the Normandy's systems, I wasn't actually angry at you, I may have just wanted to watch your squirm.

"Have I ever mentioned that you're such a mean person sometimes?" Joker asked as he wiped a tiny bead of sweat from his brow.

"I don't know, but would you mind if I told Shepard about your fornax col-"

"I'm shutting up now Tom!" Joker said as he rolled his eyes.

"I think I'll be in the war room now so if Shepard wants to see me just tell him I'm in there if he asks alright?"

"Yeah, it was nice having you in the cockpit for a couple months."

"You too Joker, see you later."

In truth the war room had way better seats, plus it Tom felt way safer in there knowing he was pretty much smack dab in the middle of the ship, plus he had two alliance soldiers camping out at the door so he would feel doubly safe.

Shepard happened to be in the war room at that time. "Hey Tom." He said.

"Hey Shepard, what are you doing right now? Just curious."

"I'm just thinking about our war assets, the reapers are an incredibly powerful fighting force, can we ever truly fight them and win in a conventional fight?"

"We will Shepard, with your leadership I don't doubt it, that also reminds me, where are we going right now?"

"We're going to a school that a fake distress call responded to, it seemed like the kind of shady tactics the Illusive man would pull so that's why I decided to check it out, will you be alright after that surgery?"

"I'll be fine, the surgery was pretty small scale so I shouldn't have any problems since I've pretty much recovered from it at this point."

"Good to know, I-" Shepard was inturrupted by Joker. "Hey Commander we're pretty close to Grissom Academy, you might want to come see this."

"That's my cue, see you later." Tom nodded at this.

XXXXXXXXXXXXXx

Shepard entered the cockpit, and just like he expected, Cerberus vessels were docked at multiple ports.

"Shepard we're recieving an emergency signal from someone on the ship."

"Patch them through."

"Hello? Is anyone there?"

"I'm Commander Shepard of the Normandy, I'm here to help."

"Thank the lord you're here, I'm Kahlee Sanders and Cerberus has been trying to take the remainder of my students, they've locked all communication to the outside and have shut down all remaining ports."

"How are we going to get into the school then?"

"There's a very small cargo bay near me that I barely have access to, but Cerberus has several fighters guarding it so we'll have to think of something else."

"Negative, Joker will distract Cerberus while my shuttle docks unnoticed, from there I'll come to you alright?"

"Yes Commander."

"Garrus, Kaiden and Tom please report to the shuttle bay with full combat gear."

...

XXXXXXXXXXXxx

"Wait so we're raiding a Cerberus controlled base?" Kaiden asked in the shuttle.

"It was originally an Alliance school, but now it got taken over by Cerberus, we have to rescue the remaining students and teachers while taking out and Cerberus troops in our path, am I clear?"

"Yes Commander."

"Okay, the Normandy will distract the Cerberus fighters while we sneak on, our first objective is to find Kahlee Sanders and then to find out where all the students are. We should be landing in 3 minutes so be ready."

The shuttle ride was uneventful, which was a good thing since it meant that Joker was doing his job distracting Cerberus, they landed in a relatively small shuttle bay, but being the pilot Cortez was he managed to easily squeezed the shuttle in there.

"Keep the shuttle in position!" Shepard ordered Cortez

"I'm holed up in the server room around the corner, be careful as Cerberus troops are trying to get into it right now."

"Copy that Sanders, we'll engage them immediately." Shepard said.

The next hallway had four Cerberus troops who were all killed easily as they were taken by surprised and didn't get into cover fast enough.

"Sanders, we're clear, it's me."

"Thank you for coming, I don't think I would've been able to take those troops for much longer with out your help."

"Where are the rest of your students? And how many students are still here?"

"There's fewer then 20 students, and most of them are in various locations around the school. They're probably in groups so finding them will be easy, it's just getting them out the tight spots their at with Cerberus will be the main issue, although I believe that most or all of my biotic students are stuck in Orion hall, you might need to find them before anyone else."

"No problem, my team will deal with it, just point us in the right direction."

"You should be able to find them by continuing down that hallway, it'll eventually lead you to them, I'll unlock the door, just keep in touch with me."

"Ok, see if you can regain control of some of your systems while we're gone."

"Alright, and thanks Shepard."

"Don't mention it."

The inside the next hallway there was a nice view of a student getting dragged by his legs, Cerberus troops were carrying him to a shuttle, Shepard watched grimly before moving on. Inside the next main area there was one biotic student.

"Reiley Bellermine, drop the barrier, now!"

Shepard nodded towards Tom and Garrus, who both pulled out their sniper rifles.

"I can't do this! You'll hurt me!"

"Mark!" Shepard shouted, right at that moment, three out of the four Cerberus troops heads just exploded, and the last one was tossed by a pull and then shot.

Reiley dropped the barrier as soon as he realized that Shepard was part of the Alliance.

"Hey, are you alright?"

"Yeah, I am, but my sister is a littler further ahead, can you please rescue her too?"

"That's the point of me being here, you should get back to Kahlee Sanders, she's in the server room down that hallway."

"Thank you for helping us, I don't know what I would've done without your help." Reiley said as he started walking towards the hallway Shepard had pointed to.

"Cerberus really wants to indoctrinate these guys don't they?" Kaiden said, it was a statement, not a question.

"Their good people, I'm not surprised they've caught the attention of Cerberus, let's make sure they don't get anyone." Garrus said, his voice had a hint of conviction.

"It doesn't matter why Cerberus is here, we have one mission, stop them from taking the students." Shepard said.

* * *

A/N: Sorry for mixing up the last chapter with the first one, I really wasn't paying attention there, sorry about that! This chapter was mainly filler, besides the last part with the Grissom Academy. Every story has at least one of these, I guess this one was mine. My thanks goes out to the four people who pointed it out in reviews as I would never have noticed without them, see you next chapter!


	7. Chapter 7: Playing Hero

"Stay back! Or I'll... I'll." The girl looked exhausted.

"She doesn't look so good." Tom said.

"Seanne, can you hear me?"

"How do you know my name?"

"I saved your brother, he's with Kahlee Sanders at security, can you make it back?"

"Yes, I can, thank you for helping me, I'm just going to rest for a minute."

Kahlee Sanders contacted Shepard as soon as he exited the hallway where Seanne was.

"Shepard, can you hear me?"

"Loud and clear."

"I just received an emergency message from the students holed up in Orion hall, an instructor is with them, but they won't be able to hold out much longer."

"We're almost there, we'll be able to assist soon."

An intercom activated and instead of the Cerberus announcer who's announcements were getting increasingly annoying Kahlee Sanders was on, which was likely to give the students a beacon of hope. The next door actually was the entrance to Orion hall, which was convenient since Shepard had no idea how close he and his squad were to said hall.

"Jack?" Shepard asked, surprise evident in his tone, of all places this was the least likely place Shepard would've expected Jack to be.

"Shepard?" Jack was about to say more, but she had to rush to another student who was about to be shot by a Cerberus Atlas.

"Everyone get up stairs this thing's outta your league, Shepard keep this thing off us!" Jack as she ran up the stairs along with three other students.

"Garrus, Tom, Kaiden use overload on that Atlas!" Shepard shouted before gunning down a Cerberus trooper.

The combined efforts of three overloads at once effectively halved the shield strength of the Atlas, but then it retaliated by firing a missile which pinned down Kaiden and Tom.

"Kaiden, keep that Atlas distracted, I'm going to cloak and flank it!" Tom said.

"I got you covered!" He shouted back before hitting the Atlas with another overload.

Kaiden did a pretty decent job distracting the Atlas, so the Cerberus guy inside didn't notice when there was one less guy in cover.

Tom had a pretty devious plan. His cloak lasted just long enough for him to get to where Garrus and Shepard were, they were both pinned down by an engineer with his turret and several Centurions.

"Hey uh, Shepard can I borrow a grenade?"

"Why do you need a grenade?"

"You'll see in a few seconds, just please give me one, I assure you it's for a good cause."

"I don't doubt that, I just don't want this grenade to be wasted."

"It won't be, you'll see, bye!" Tom cloaked again after that statement. He ran all the way across the battlefield and got behind the Atlas mech, the machine's shields had finally gone down after four overloads from Kaiden, making it easy for Tom to pulled the pin on the grenade and stuff it in the power generator thing on it's back. The resulting explosion was huge, creating a massive fireball.

The fight immeditely tipped in Shepard's favor after this as the turrent the engineer had set up couldn't shoot two groups of people at once and, after about twenty seconds got destroyed because it couldn't take the combined fire of four hyper lethal soldiers. The engineer and two Cerberus troopers that were still alive were easily killed when their fire support was stolen from them.

Right after that a door opened on the left and several more Cerberus soliders piled on into the room, the reinforcements had arrived a little late to help their friends, there were no Centurions among them, which made them easy pickings for a skilled sniper, and everyone in the squad except Kaiden was armed with one, so you could image how the resulting firefight went.

The Cerberus squad got slaughtered, their squad was destroyed slowly as the troops died one by one, most of them died by sniper rifle head shots, but Kaiden did sneak a kill or two in there, Tom was glad when it was over, he was low on ammo.

"Kahlee said she was putting out an SOS, and I didn't think the king of the boy scouts would show up." Jack seemed very happy to see Shepard, she didn't miss a beat with her students though. "Alright, amp check! Prangley those fields were weak! Cerberus is going to lie down and let you take them like the girl you took out to prom. Now grab some juice and an energy bar, we move in five." Jack jumped off the balcony after that and went up to Shepard, and then she punched him in the face.

"This is what you get when you trust Cerberus, Shepard."

"You think I didn't notice Jack? I was only working with Cerberus, not for them, and Tom here would vouch for me secretly not trusting Cerberus, believe me when I say that me and him have had several discussions of why Cerberus is a terrible organization."

"I kinda will vouch for him, still good to see you though, Jack."

"Oh hey Tom, still hiding behind on those fancy gadgets that make you useful?" Tom inwardly sighed, but hey, this was to be expected, Jack hadn't changed a bit.

"Anyway, right now all I care about is getting my guys out of here."

"Your guys?"

She chuckled. "Yeah I guess so."

"I guess it's nice to see you've turned over a new leaf, did my leadership rub off on you?" Shepard smirked at the last part of that sentence.

"Well, while you were off playing hero the Alliance brass sought me out, they offered me this position after I demonstrated what I was capable of, and apparently my students responded well to my teaching style."

"The psychotic biotic." One of the students said cheerfully.

"I will destroy you!" Another one said.

Tom wasn't listening however, Section had just decided to start talking, he still hadn't gotten a synthesized voice yet, but that was partially for the best, it would be a little hard to explain to a passersby if his Omni-tool suddenly started talking.

 _You know, if you could get some medigel I could help gradually introduce it into your body if you were shot while your shields were down._

Tom muted the microphone on his helmet, he didn't want to sound insane to his fellow squad mates. "I might be able to get some, but only if no one else needs it since I don't want to take some if Shepard can get his hands on it since he would probably do more good with it then I would."

 _You would only need a four vials of it to stop a body wide injury. I searched the extranet and it seems that even a small vial can stop the bleeding of a wound that is significantly bigger, so do try and find some if you can._

"We'll see Section, you were a little quiet on my last mission, were you uh, thinking or something? I don't know how you 'think' so don't quote me, what were you doing?"

 _I was running extranet searchs, deliberating with EDI an-_

"Wait a second, you were having a discussion with EDI? How the hell did she even know that you were on my Omni-tool?"

 _It was simple really, she sought me out after our discussion with Shepard in the cabin, it's fascinating to meet another AI, it was nice to talk to someone that wasn't slow._

"Hey! I'm not slow, I'm a prodigy in computer sciences, don't call me slow."

 _Well, you organics process things much slower then that of an AI, that's not teasing, it's a fact._

"Well that may be true but don't be snobbish about it like that, I understand that it is actually a fact, but it's an organic thing, I would've considered that an insult, search that up real fast and you will know what I mean. This converstation is over anyway, Shepard just got done talking to Jack, and I'll see if I can get some medi-gel, alright talk to you in a bit."

Tom un-muted his microphone right after that. He also found four spare thermal clips lying around from some dead Cerberus guys.

"Alright gentlemen, our job is to get these students out of here, but I'm sure you've already heard me talking to Jack so I'll skip the details, just stay here, I'm going to go re open the door you see behind me." Shepard jogged upstairs where he released the lock on the door.

"Shepard, we'll go up above on the catwalk while you draw their fire down there, you better do your jobs too or I'm kicking all of your asses!" Yep, classic Jack. Shepard came back downstairs quickly after that.

"You heard the lady, let's move!" Shepard could really be a drill Sargent sometimes.

The next room was a pretty neat looking one, it was huge in scale, it look like a park on Earth or something, complete with grass, several walkways and a small river that cut off the room into two sections, although there was a smaller room on the side that connected the two parts of the bigger room. Tom hated this part of the mission because the Atlas on the other side of the room would have you pinned down while the Guardians would close in on you from both sides, fortunately Shepard was using his head.

"Tom, activate your tactical cloak and flank those Guardians, Garrus keep their heads down with that sniper rifle of yours, and Kaiden... on me, now get into position people!"

The tactical cloak was a huge help in killing the Guardians as they couldn't see Tom at all, and it was easy as pie to get back stabs since the Guardians only had a pistol and not an assault rifle so they didn't put as many rounds down range as a standard Assault trooper did, but he still avoiding sprinting right in their line of fire as their pistols were deadly at close range. He killed around 4 Guardians and an Engineer, he could only get stab kills as using a gun would break his cloak, and although he got a pretty significant damage when breaking from cloak to attack he would be right in the line of sight of the Atlas so he didn't risk it, Garrus got several head shots and got a lucky kill on a Guardian because the guy was stupid enough to walk over a proximity mine.

Shepard and Kaiden were a really good team as they had all the powers at their disposal, Kaiden had some tech and biotic powers while Shepard had all the guns, there was also the added bonus of Jack's squad of students who would be able to throw an occasional warp down range which would force some troopers to combat roll out of cover where they were easy pickings for Shepard, Kaiden or Garrus.

The battle took a lot longer then a lot of the previous ones, mainly because the Cerberus soldiers were at near platoon strength, but half of their squad was at the unreachable other side of the room so it was easier then expected.

"Great job team, now let's get to the other side of the room and deal with those engineers and Atlas mech." Shepard said.

Inside the small room were a couple of things, some computers, an armor piece which Shepard made a beeline to almost immediately and a box containing medigel.

"Is anyone taking this?" Tom said out loud.

"I've got a full capacity of medigel, you can take that." Shepard said.

"Thanks." Inside were three vials of a blue gel, and another vial with a white fluid inside of it.

 _Insert the vials in these sections of your body, I've highlighted them on the diagram on your HUD._

There were two slots on the sides of his legs, and two on his back. They fit in the slots easily as Section sealed the medical injection points.

 _If you are shot I can now provide a dose of medi-gel to various parts of your body, headshots are still lethal however, you are not invincible._

"Tom cloak and scout ahead, I have no idea what they've set up out there." Shepard ordered.

"I'll check now, someone here has to exit with me however, because a door opening and closing would seem pretty suspicious.

"I'll roll into cover as soon as the door opens." Kaiden offered.

"Good idea, keep your tech armor up, I don't want any casualties, I'd rather put my own life on the line then any of yours." Shepard said.

"I'm ready when you are, Kaiden." Tom said through the comms."

"I'm opening in 3...2...1...NOW!"

Kaiden got into cover immediately, but even in that one moment his shields got cut down by 20% as several turrets honed in on his position, his cover was pretty solid though, so he was safe, for at the moment at least.

"They've got like three turrets and an Atlas mech, but they don't have any Centurions, they have one Guardian and several Assault troopers, and a a lot of engineers, plus they can shoot you from a level above so be aware of that, Kaiden you're still fine however as they can't get a good angle since a guard rail is blocking their line of sight."

"Copy that Tom, your orders are to cause chaos on the upper level and prevent them from gaining a height advantage." Shepard commanded expertly.

"Will do Commander, I'm moving now."

It was very easy to get to the second level as everyone was focused on Shepard, Kaiden and Garrus as they laid down suppressing fire and kept most of the troopers from focusing on anything else.

He killed three soldiers with back stabs before anyone even knew he was there, the remaining engineers fought back, and Tom found himself pinned down right at the entrance to the next hallway. He killed one while the guy was setting up a turret with an overload which caused the machine to blow up in his face, the second guy died to a Widow round to the face and the third guy wasn't watching his flank and got shot by Garrus who capitalized on the engineer's exposed backside.

There weren't any troopers left after that last engineer, there was just one turret and the Atlas which was taking heavy fire. Tom easily dealt with the turret as he had Section hack the thing to turn it on the Atlas until it severely damaged the mech, and then Section set it to self destruct.

"Good work team, let's keep moving, we're doing great so far." Shepard said.

* * *

A/N: I actually loved the Grissom academy mission, it's probably one of favorite missions in the entirety of the series, I hope the people that enjoy the action got a kick out of this chapter, as there's more of that coming! I decided to start including Section a bit more because he's a bit of a wildcard, and I like writing about those kinds of things. This is an early post because I feel like some of you guys just can't wait for the next one, I hope you enjoy this chapter, as I've got lots more coming.

 **Reviews:**

BrotherCaptainSheperd: I'm like 89.1337% sure that you enjoy playing Mass effect Full renegade.

redcollector: "Ask and it will be given to you; seek and you will find; knock and the door will be opened to you." - The Bible Matthew Chapter 7 Verse 7

general-joseph-dickson: Support is appreciated!


	8. Chapter 8: 25 Cents

"Hold on for a second, I have to do something real fast." Tom said.

"What are you doing?" Shepard asked, but that question was answered when Tom took his helmet off.

"Geez that thing stinks, I don't I would've lasted much longer without having to puke."

"Enough delay, let's keep moving."

The hallway Shepard and Co. entered some students behind some sort of barrier with Cerberus troops attempting to coax them out.

"That's an impressive barrier Octavia, our files say you've been working on shield technology, Cerberus could use you."

"Back off, ass I'm not joining a terrorist group, this shield is cyclonic barrier technology, it'll hold off your guns for hours."

Shepard nodded "Sneak up behind him with your cloak, I'll snipe the guy you don't get." He whispered. Tom did exactly that, he cloaked, snuck up behind on of the Cerberus troopers and stabbed him in the face, the other guy reacted quickly, but not quickly enough as he got a bullet to the face before he could try anything.

"Who are you people? I didn't trust the last group and I have no reason to trust you." Shepard walked out from behind cover.

"I'm Commander Shepard, and this is my squad of Alliance Soldiers that are going to get you out of here."

"You guys look legitimate, but I still don't think I can trust you." Octavia said reluctantly.

"It's not about trust, it's about getting everyone out of here safely, I'm not going to put up with this, Tom deactivated the shield."

Tom tapped a few buttons on his Omni-tool and the barrier deactivated safely.

"Nice barrier kid, just try to make it a little more resiliant to hacking attempts next time, Kahlee Sanders needs you guys." Tom complimented.

"Uhh, thanks I guess?"

"Kahlee needs you two, get to the shuttle bay as soon as you can." Both of them ran down the hallway.

"Some of this tech is very advanced, these students are really smart." Tom said as he scanned the device that the students were using.

"Anything useful?"

"The device itself shows some interesting things, but the schematics that have been downloaded onto it are extremely useful, I just don't understand why they put the schematics of the device in it's memory, but I'll take it anyway, it could definitely help us later."

"Good idea, it might be useful later." Shepard said.

"I got it, let's keep moving."

Down two more hallways, and through two more doors and they finally located the shuttle bay, but they also found a Cerberus engineer that was unaware of the squad's presence. His head didn't last long after taking three high velocity sniper rifle rounds to the face.

"Now the bigger question is who gets to ride in this thing?" Garrus asked.

"I'm more handy with a gun then a mech so I don't think I'll take it." Shepard said.

"I can't use my biotics while controlling something else, I'd rather not." Kaiden said.

Garrus looked at Tom, and Tom looked at him.

"I'll flip a coin gentlemen, we have to solve this like civilized people." Shepard said as he pulled a quarter out of his pocket.

"Why do you have a quarter on you? Those things are centuries old!" Tom said, he was surprised there still were coins like that in existence in this day and age.

"It was a family tradition to pass this on, my mom passed this on to me."

"How does this work exactly? I still have no idea how this is going to work." Garrus said.

"Garrus you choose a side, heads or tails and then I flip this coin, the side that's facing up is the side that wins, and the person who chose that side gets control the atlas." Shepard explained patiently.

"That seems fair enough, I choose tails." Garrus said.

"Heads all the way."

Suffice to say, Tom was going to have lots of fun today.

Shredding Cerberus troops with huge guns was funner then Tom would've liked to admit. He didn't enjoy killing people, he only did because he had to. He didn't mark up his kills like it was a high score or brag to his squad mates about how good of a shot he was, he did it all because it was necessary. But seriously though, blasting people away with huge guns was fun.

It was easy to protect the students as they ran to the shuttle bay since the Atlas could take a huge amount of punishment and dish out twice the amount it had taken. And since there were little Centurions on the battlefield most of the Cerberus soldiers weren't coordinated at all, they just threw their bodies into the fray where they were shot immediately or picked off by a sniper.

After a while however Tom realized there was only one student was left, and she was a little late since she was the only person not in the shuttle bay beside himself. The Atlas was taking a lot of health so he decided to abandon it to provide a bit more mobile covering fire.

"Rodriguez! Get over here! I'll cover you!" Tom shouted before spraying an Assault trooper with his Mattock.

The girl managed to make it all the way to Tom without taking a single shot, she ducked behind cover just as her position was peppered with bullets.

"Get behind me, I'll cover you!" Tom shouted before rolling out of cover and making his last stand as he shot several troopers.

As soon as she got safely to the door of the shuttle bay Tom slowly backed up while covering himself. He made it to the entrance of the shuttle bay without losing his shields where he jammed the door to stall Cerberus.

"Tom! Get the hell over here!" Shepard shouted and Tom had no interest in disobeying his orders.

He ran as fast as he could and jumped onto the shuttle just as Cerberus managed to open the door he had jammed.

"We're clear, get us out of here!" Shepard shouted.

They were gone before Cerberus could fire another shot.

"That was too close." Kaiden said quietly.

"Try not to risk your life again Tom, I'm not losing another crew member, not after Virmire." Shepard said the last part of that sentence solemnly, like he was regretting something.

Jack didn't seem to catch onto the mood however as she was talking about something joyful as soon as she entered the passenger part of the Cerberus shuttle after checking in with Kahlee Sanders who was piloting said shuttle.

"You guys kicked ass out there! When we get to the Citadel your all getting inked, my treat." She paused for a second. "What do you guys want? An ascension logo? A biotic fist? Maybe a unicorn for Rodriquez?"

"Screw you ma'm!" Rodriquez said, although her tone was playful.

"Is anyone hurt?" Shepard asked.

"We're all good Shepard, although I'm not surprised you care you pus- hero."

Shepard smirked. "So, you stopped swearing as much huh?"

"We asked Jack to restrain herself when it came to teaching to ensure a healthy teaching environment." Kahlee Sanders said over in the pilot seat.

"So a swear jar huh? I'm pretty sure if we emptied that we'd be able to get another Normandy, and that's from your swearing on the school alone, we're probably be able to buy the rights to a planet with all of your swearing on the Normandy SR-2." Shepard was grinning like a manic now.

Jack looked around. "Cover your ears kids."

"Hey Shepard, fu-

 **The next paragraph was removed from the story due to excessive swearing from Jack.**

...

Now Tom knew why Bioware had cut that scene from the game, there was so much swearing that they probably would've been able to buy another Normandy if Jack actually had a swear jar. Fortunately Jack said that was 'just for fun' since she hadn't swore like that since the last time she was on the Normandy. She needed to get it out of her system.

These were the thoughts going through his mind as he stood for a security scan from the two Privates that were still camping the door, which still made no sense because there was nothing to steal in the war room.

For now he could sit down at a terminal and browse the Extranet for anything cool, maybe he could pirate a few games if he really felt like doing something other then saving the Galaxy, but there was something he had to do first.

* * *

To: Commander Shepard

From: Tom Fisher

Hey Shepard if you want to chat with me a bit I'll be in the war room, I've moved there since EDI took the co-pilot seat but you probably already know that, I was wondering if you wanted to talk about Earth since that's been a bit of touchy subject for me and I'd appreciate it if you'd talk to me about it.

* * *

...

"Hey Tom, you wanted to to talk?" Shepard asked.

"Yes, just hold that thought for a second...there we go! Okay, can you tell what's happening to Earth? I never got to see it before the reapers hit and I haven't seen any statues reports from anyone anywhere."

Shepard sighed. "I'm not going to lie to you, it wasn't good, they decimated our fleet before getting to Earth and once they got to Earth it was a slaughter, they've probably killed billions of humans by now, Earth is barely holding up any resistance at all."

"After seeing the situation on Palaven I've been wondering how Earth has been doing, it doesn't look good."

"The devastation you see on Palaven? It's double that for Earth, to be honest it makes it hard to think about how we could ever win this war."

"Don't lose hope Shepard, you've defeat Saren and Sovereign, you died and then came back to crush the collectors, if anyone can win this war it's you Shepard, you can't lose faith now."

"Thanks, it's good to know that even when I'm facing hell itself, I've got people like you covering my back."

"You can count on me Shepard, there's no doubt about that."

"Thanks Tom, now I've got diplomats to deal with and I can't talk any longer, and also there's one other thing I have to tell you about."

"What is it?"

"The crew is having a gambling match down in the crew deck, you were invited to join, I just thought I'd pass along the message since I don't gamble unless I'm celebrating something."

"That actually sounds fun, I'll be down stairs then."

...

"Here comes trouble." Garrus said as Tom walked into the lounge.

"Hey guys! I'm here for the gambling match Shepard said you guys had going on."

"About time you got down here, now we're just waiting on Ken, and Chakwas until the game starts, how many credits are you going to start with then?"

"I'd say about 250 credits, is that too high? I feel like that's a bit high."

"Well James here decided to throw in 300 credits, he seems a bit confident." Gabby said.

"Hey, I know I'm going to win, I may as well throw a lot of credits in to get a good payout."

"You seem a bit cocky James, let see if you can walk the walk after talking the talk." Kaiden said.

"I hope I didn't miss anything, I was just ensuring that Mordin had all the equipment he needed." Dr. Chakwas said as she entered the room.

"Well, James here thinks this game is already in the bag, so I have no idea if this some pre-game psychological warefare or something."

...

Well, James WAS winning, until he and Garrus got called for a mission, which took them both out of the game. After that Chakwas took the lead with around 500 credits with Tom in third place at 325 credits, the game ended there because no one wanted to bet anything because Chakwas was winning almost every round and no one would even come close to stopping her.

"I never thought you would have a really good Poker face Chakwas, and you always seem to know when to bet and when to fold." Tom stated.

"It was just a skill I was naturally good at, no one expects me to be good at gambling which is why I usually win, everyone underestimates me, and having a good Poker face helps."

"Well you certainly surprised me, see you later."

Tom decided to get back on his console for one or two hours and then hit the sack since he was somewhat tired and he needed to work off the rest of his energy.

He sat down at his terminal after a long elevator ride up with two other people. He was about to 'work' by browsing the extranet since he had nothing to do but he actually got a call from Kaiden, which was something he was not expecting.

"Oh uh.. Hello Kaiden."

"Hello Tom, how are you doing?"

"Just fine, you already know how our little gambling game went."

He Chuckled "Chakwas packs a punch doesn't she? The only reason I managed to stay in second place after Garrus and James left is because I've played Chakwas before and I was expecting it."

"Welp, anyway is there something you want to talk about? Besides the rubbing in of you finishing in a higher place then me?"

"I was just curious about your past, out of all the people on the Normandy I know, you're the most enigmatic."

"I suppose it's fair enough, I was recruited by Shepard for the suicide mission which isn't actually that dangerous since everyone survived the mission, I was born on Earth, I was an orphan but I worked my way up to having a respectful family, until they all died from some blue suns who decided they were cool I...I still miss them to this day." Faking tears was somewhat hard but Tom knew how to do it, he was a good actor after all.

"I'm sorry if I dug up some bad memories for you to relive, that most have been painful." Kaiden said sympathetically.

"I just need to sleep this off, I'm sorry it's just that memory is super painful, I should go..."

"Okay."

Tom hated this, he hated lying to the crew like this, he hated it, the secrets were tearing apart mentally inside, and it disgusted him, honestly wasn't what he always liked to do but this was a new low, he had to sleep off the guilt because in reality that's what it really was that was hurting. He slept a very guilty man that night cycle.

...

"Tom can you hear me? You need to wake up."

"Ugh, what is it?" The figure came into focus, it was Dr. Chakwas.

"Shepard needs you for a mission he just called you over the intercom."

"Did I really sleep that long?! I'll be right there."

* * *

A/N: I hope you've enjoyed this chapter! Unfortunately I will not be able to post a chapter next week as I'm going to be gone for a week, so I hope this chapter can entertain you until then.

Reviews:

 **BrotherCaptainSheperd:** Badass alert class! We've got a potential badass here!

 **redcollecter:** On that we can agree

 **Dickson:** Thanks for the support!


	9. Chapter 9: Mortal

Yes, I am allowed to post chapters this early!

* * *

"Take point up ahead Fisher, do some recon for me." Shepard commanded.

"Yes sir." Tuchanka was an ugly planet, that was for sure, playing the game was one thing, but BEING there? It smelt like death, and it was not pretty to look at.

Shepard had briefed him on the situation, they were disarming the bomb to prevent Cerberus from shattering the fragile relationship between the Turians and Krogan forever. Up ahead was a very heavily fortified area, there was a turret set up by an engineer, several Cerberus troopers and a Nemesis.

"It's heavily fortified, they've got some sort of sniper, and her gun is similar to mine, and they have a turret set up. They've also got a handful of Assault troopers and an Engineer."

"Copy that, you're job is to take out that Engineer, after you do that we'll open fire to cover you so that you can get to cover."

"I'll overload his shields, and then take him out, on my mark." He started counting. "3...2...1...Mark!"

The Engineer went down instantly, he had absolutely no time to act as his only line of defense was stripped from him, followed up by a quick head shot. It was mayhem after that as Shepard and co. and the Assault troopers opened fire.

Tom managed to get into cover, and when the gunfire on Cerberus' side ceased he peeked out, only to get his shields decimated by the turret which was still functioning. He attempted to duck, but he was too slow Nemesis got a clean shot right into his shoulder, which incapacitated Tom. The pain was brutal, Tom's left shoulder felt like it was on fire, even though the bullet wound was small it had done significant damage to his shoulder. But he had fallen behind cover, so he was safe, for the time being.

Shepard couldn't even see Tom from where he was at, so he didn't even know that Tom was down.

The only thoughts swimming through Tom's head was that it was over, he was going to die, right here, either by bleeding out or by the Nemsis alerting her squad mates to dispose of him, he never though it would end this way. That's when Section saved his life.

 _I'm going to inject you with some epinephrine, and release a dose of Medi-gel in the area around your shoulder, it shouldn't substitute for full scale surgery, but it should stop the bleeding and get you back on your feet, I'm using up 50% of it, that should last you for a while._

The effects of the medication kicked in instantly, and Tom was back on his feet in less then a minute, and by then the only enemy that was alive was the Nemsis which did not expect to get shot in the side of the head, she had assumed that she had killed that guy.

Tom muted his microphone on his helmet. "Thank you, you may have possibly saved my life."

 _I'm just doing my job._

"How are you up and walking? That shoulder wound should've incapacitated you." Shepard said, worry was evident in his tone after seeing that shoulder wound.

"Medi-gel and maybe a little dose of adrenaline got me back on my feet, I'll have it looked at when we get back to the Normandy." Tom seemed calm on the outside, but on the inside he was gritting his teeth, that wound hurt, even with the Medi-gel sealing the wound and a does of epinephrine flowing through his system it still ached and he couldn't rotate his arm very much or it would hurt a lot more.

"They're retreating, I don't like the look of this." Shepard said, paranoid. The shuttles flew away, leaving a sense of foreboding in most of the squad, Tom already knew what was going to happen so that was a comfort to him. They eventually reached the bomb after a short walk.

"That bomb is huge." Liara said.

"If this bomb detonated it would cause countless casualties and destroy 95% of the land mass in this area." EDI said. Tom grimaced, that was definitely not a good thing.

"Let's get over there, the Turians are going to need our help."

"Commander Shepard, I'm glad you could make it." Victus seemed relieved to see Shepard.

"Will you be able to disable this bomb quickly?" Shepard asked.

"I'm going to have to created a bypass, that'll take time."

"How long?"

"About 10 minutes, it shouldn't be too long." Just then, one of Victus' men got shot in the back.

"That's too long, I'll have my best hacker take a look at it, he'll be able to do it much quicker then you would be able, I need you to defend him."

Victus looked crushed. "But I-"

"This isn't the time for arguing! Tom can get past it much faster then you would, and he needs protection while I face those Cerberus goons head on, do you understand?!"

Victus nodded. "Yes sir."

"Good, now cover one of my best men." Shepard said before jumping over a ledge to engage Cerberus.

"Victus I have a question for you." The Turian spun around.

"How good of a sniper are you?" Tom asked.

"Decent."

"Take this thing then." Tom handed him the Widow.

"Good luck! I'm going to hack this bomb now."

Hacking the bomb was easy, it was just that Tom knew the trap that Cerberus had planted so he coded a command into the bomb's interface. It was basically a script that said 'If x does this, execute n' in this case x was the bomb counting down and n was to drop the trigger mechanism, it was a pretty smart idea. So when he did use his pre-coded bypass to break the encrpytion on the bomb, he executed the command as soon as he saw the countdown.

"Bomb is disarmed." Tom said as he drew his Mattock and started laying down cover fire to Shepard's squad as they engaged Cerberus.

"Shepard, bomb is defused, there was a trap to set the bomb to blow up if a disarm operation was tried, but I stopped it."

"Copy that, the cover fire is appreciated, please continue to lay down fire as we finish these guys off." Shepard said.

Cerberus retreated soon after they realized that there was no point to continue fighting because the bomb had already been disarmed. Or maybe they were just sending more troops to attempt to kill Shepard which was kind of sad, considering they were sending those men to their deaths, and Cerberus should've seen that the bomb's trigger mechanism was not on the bomb. This disgusted Tom, why would they waste their own people like that?

"They're backing off, good thing we came prepared." Shepard said.

"Commander, I am in your debt, without you would never have been able to disable this bomb." Victus said.

"We can go over this later Victus, lets just get the hell out of here before Cerberus decides to throw some more troops at us." Shepard said, all business. This was a good thing for Tom too, since the adrenaline had worn off and his shoulder once again felt like it was on fire, he didn't feel very good either, he almost felt delirious.

"Victus I have one question for you..." He slightly slurred the 'you' but Victus ignored it.

"And what is that?"

"Can I... have my..." All the colour drained from Tom's face as he collapsed, but at least he got the last part of his sentence in.

"Sniip-r rif..." He fell unconscious.

...

Everything was blurry. His shoulder hurt like hell as well. "Chakwas, I think he's waking up."

"Oh dear, you just laid him down! I better dose him with another painkiller, if he woke up now he would just cause himself more pain and suffering."

Suddenly everything felt fuzzy as Tom felt a foreign substance flow through his veins.

"That worked, can you tell me why he's like this?" Tom fell unconscious after this statement.

XXXXXXXXXXXXX

"His wound seems to have gotten infected, which is strange, considering that he had Medi-gel protecting it, do you know what shot him?"

"I believe it was a Cerberus sniper, why?"

"It seems from these readings that he has some radiation in his blood, he may have been hit by a sledge hammer round from that sniper, and back in the day that ammo was covered in polonium, which was meant to cause radiation sickness in the receiver."

"Will he be alright?"

"That adrenaline that seems to have worn off will have stopped it in it's tracks for about 45 minutes, but it would come back right after that, which is probably why he fell like that, he'll be fine with a drug I have here which will cure the disease, but he'll be out of action for a while since these pills make you extremely lethargic, the bullet wound should be easy to surgically remove.

"At least he'll get better, watch over him for me doc, he's a good man."

"That's my job, and you of all people should know how good I am at it, Shepard."

"I should go now, I have business to attend to."

"Commander."

There wasn't actually any business Shepard had to attend to, he just hated seeing his crew members like that, back when he was allied with Cerberus Garrus was a constant reminder, to him it felt like a beacon broadcasting his failure to keep Garrus safe, no one blamed him of course, the issue was the he was blaming himself.

Why did he have to be a hero? It felt like he was the only one actually doing anything in this bloody galaxy to ensure that everyone saw the next sunrise, it was exhausting and mentally taxing to play diplomat for 15 minutes and then shoot someone up 20 minutes later, he hated doing it, there better be a good reward for it at the end of all this.

At least he had people like Admiral Anderson and his crew to look to, they meant more to him they anyone else in this stupid war. If only they had listened to his warnings three years ago they might of been able to save more lives, at least Garrus had been able to do that, with enough shouting of course. He didn't even realized he was there until Specialist Traynor called out to him.

"Shepard are you alright?"

"Uh wha? Oh I'm fine, just think about some things."

She shot him a look. "You have some new messages at your private terminal."

"Right."

There were several of them, but he was barely paying attention, know he wouldn't get any work done if he went on like this, Shepard excused himself from the CIC and went up to the Captain's cabin, he needed some rest if he wanted to keep a level head.

XXXXXXXXXXXXx

...

Tom didn't have a pleasant sleep, because he had a nightmare about drowning, which was pretty random. He woke up hyperventilating, and a shot of pain ran right through his shoulder at the sudden movement of his body.

"Oh dear, are you feeling alright Tom?"

"Just a bad dream, besides that I have some pretty bad shoulder pains, and I just don't feel right."

"That's because you have some moderate radiation poisoning, here take these pills, they should help."

Tom swallowed the pills, along with a whole glass of water unceremoniously.

"Thanks, why did I get radiation poisoning again? I thought I fell unconscious from a bullet wound."

"Sadly, that bullet was a Sledge hammer round, which is coated in a poison to make it a bit more lethal, which is odd, since I haven't seen that type of ammo since 3 years ago when Shepard was chasing down Saren and things were much simpler."

"Wasn't that like 3 years ago or something? That ammo is pretty old."

"It is, I'm still wondering how they adapted it into today's weapons, since that ammo was pretty cumbersome."

"So how long will I in the medbay for?"

"If all goes well then less then 5 days, but if there's complications you might have to stay for the entire week, but I doubt that. The surgery will be happening tomorrow to remove that bullet, so just rest for now."

"I think I'll do that, I don't feel very energetic anyway." Tom laid down, he could rest for now, which was all he needed.

XXXXXXXXXXXXXXXXXX

...

"Wrex keep going, the bridge is out, but don't let that stop you, just GO!" Wrex heeded Shepard's advice and went on ahead.

"The chances of the Turians alone being capable of taking out that reaper are low, I suggest a different plan of attack when we exit these ruins and regroup with Wrex." EDI said.

"I agree EDI, although I-" a violent tremor shook the area, which silenced Shepard.

"That didn't sound normal." Kaiden said.

"Let's hope what ever's down here isn't interested in us, keep quiet as well, I don't want us to attract any attention." Shepard said, tense.

After a while of walking through the tunnels, Shepard came upon a rachni corpse.

"Wrex, we've got reaper modified rachni here, you seeing the same thing?"

"Yeah, ran into a few of them, didn't make much of a difference though."

"Copy that, we're nearing the end of the ruins, standby."

Shepard couldn't have been more happy to get out of those ruins and see the sun again, he along with the rest of the squad were also surprised when they saw some actual plant life, hadn't the Krogan destroyed most of their eco-system?

"Eve, we're seeing some actual plant life here."

"That's hope, all that's left of it for Tuchunka."

"You guys bombed most of it with nuclear fire right?"

"Yes, this place was once a beautiful planet, I hope that maybe after all of this is over that we can rebuild it."

"Sounds like a good plan, I hope you can follow through with it."

"Shepard can you hurry up? We've still have to figure out how to deal with that reaper, step on it!"

"We're coming Wrex, hold on."

Kalros was definitely active, there were tremors above ground now, but Shepard wasn't worried about that right now, there was a brute in front of him that needed to die, right now. Why couldn't anything ever be simple?

* * *

A/N: And that's a rap! This chapter was definitely more interesting since I got to show that Tom is in fact, NOT invincible like most people believe, sure he's got all the cool gadgets and stuff, but he's terrible at unarmed combat, especially when he only has his fists. And yes, epinephrine is an actually a real life thing for those of you that don't know that it's just a fancy word for adrenaline, and since Section has to have perfect grammar I was forced to not use it's simplified term. I have big plans for the future.

Reviews:

 **general-joseph-dickson:** \- This guy knows it.

 **redcollecter:** I aim to please.

 **BrotherCaptainSheperd: Don't pretend you don't know.**


	10. Chapter 10: Priority: Tuchanka

"Get your ass over here Shepard! Kalros will be back soon, and I don't plan on dying today!" Wrex shouted over the comm.

"You heard him, double time it people!" Shepard shouted as the group ran towards the tank which was waiting for them.

"Everybody in, go go go!" Shepard shouted before getting in herself.

"What about Wreav?" Eve asked.

"That pyjack was useless, maybe now we can use our food to feed more useful Krogan." Wrex said dismissively.

"So we're going to have to summon Kalros huh? Sounds dangerous, but I've had more then my fair share of danger in the past two years."

Wrex chuckled. "Haha! That's the Shepard I know, even death just pissed you off, you'll be fine at taking down that reaper."

"We're going on foot for the final stretch to the shroud, since we're smaller targets when outside of the vehicle." Shepard said.

"Old lab ahead, will use to finalize genopahage cure transmission, will finish cure from there and use old transmission strain."

"Sounds like a plan, anything else I should know?" Shepard asked, but nobody spoke up.

"Let's do this then." Everyone piled out of the tank, the reaper looked ominous, even from a distance.

"Rachni behind us!" Kaiden shouted.

"I'll take care of them Shepard, go on ahead without me, I'll be fine!" Wrex shouted before pulling out his Claymore and going to town on the insects.

"Let's get moving people!" Shepard said.

Reaper ground forces were no problem, since there weren't many of them. EDI and Kaiden had all tech and biotic powers and Shepard was packing heat, this well rounded combination resulted in the doom of the reaper's ground forces.

It wasn't fun though when the reaper started attempting to shoot Shepard with it's destructive laser beam, which almost hit Shepard on the bridge.

"Get behind cover when the reaper's weapon charges!" EDI shouted.

"But what happens if there ISN'T any cover?!" Kaiden shot back, they probably wouldn't have made it if the Turian fighters came back to distract the reaper.

"We'll keep this reaper off you Shepard!" One of them said over the comm.

It was significantly easier to progress after the reaper was distracted, but it was also significantly more terrifying being right under the bloody thing.

"Screw those brutes, just run past them with me!" Shepard shouted before dashing right past them. He almost got crushed by the feet things holding the reaper up when he made it to the first hammer. The he dashed right back and made it to the second maw hammer where he again had a near death experience by another close encounter with the reaper's crushing feet things.

"Get to the shuttle you two! I'll get the cure dispersed with Mordin and meet up with you on the shuttle!" Shepard commanded, and both EDI and Kaiden were happy to comply to the order to get the heck outta there.

 _Meanwhile_

Tom awoke again, this time he actually had a decent sleep, he didn't feel as sick as before either, but he was definitely still sick.

"Are you alright Tom?" Dr. Chakwas asked.

"I'm feeling a bit better now, and I didn't have any nightmares this time."

"That's good, unfortuenly it's the ship's night cycle now and everyone's going to be sleeping, so you might be a little bored for a while, this might keep you entertained for a while." Dr. Chakwas picked up a datapad from her desk and handed it to Tom.

"The codex, isn't this a compilation of the general knowledge of the galaxy or something?"

"Yes it is, you should fine many interesting subjects on there, that should keep you entertained for a view hours."

"Thanks." Tom hid his disappointment well, he had already seen 90% of the codex anyway, so none of this stuff should be new. More out of showing respect to Chakwas then anything else, Tom went into the know associates category, since that one was his favorite. Interestingly enough, there was actually one new one

 _Garrus Vakarian_

 _EDI_

 _Dr. Chakwas_

 _Commander Shepard_

Tom selected Commander Shepard's entry, since this one was never in the games. It made sense though, since Shepard had his own part of the codex that broke down his or her's history.

* * *

John Shepard is an Alliance Commander and Citadel Spectre. Shepard was raised on many military ships, both of his parents were in the Alliance when he was born, and he was never on the same ship for longer then 6 months since his parents transferred often. He followed in his parent's footsteps and enlisted with the Alliance when he turned 18.

Shepard was on shore leave on Elysium when the first wave of batarian slavers, warlords and criminals attacked, this attack is know as the Skyllian Blitz. Despite overwhelming odds, Shepard not only survived the attack, but rallied the civilians to hold back the attackers and when their defensive line was breached Shepard himself sealed the breach, and after hours of grueling fighting reinforcements came and the attackers fled, throughout the alliance Shepard is regarded as a true hero, this is the main reason Shepard was promoted to Commander so quickly.

Shepard is extremely proficient with all modern firearms, he is a notable sharpshooter as well, and was the first ever human Spectre. He is also part of the Alliance's N7 program of special forces, and he passed the entry exam from N6 to N7 with flying colors.

Commander Shepard is directly responsible for stopping Saren when he attacked the Citadel as well as saving the Council from Sovereign. Some of his less know missions are when he formed with a temporary alliance with Cerberus to stop the Collectors. Right now he is currently working with the Alliance and Council to stop the reapers.

* * *

That was definitely interesting to read, all things considered, he had never thought that Shepard actually had his own codex entry, but it did make sense.

XXXXXXXXXXXX

"Mordin, are you sure you want to do this?" Shepard asked.

"Yes Shepard." The elevator door closed. "Someone else might have gotten it wrong."

Mordin's elevator accelerated to the top floor, where a damaged console waited for him. "Error! Temperature malfunction detected! Error!" The automated VI said.

Mordin easily fixed this issue and entered the cure solution into the machine, there was a failsafe but he bypassed it.

"Class bypasses, old failsafe, excellent work, yes yes." He smiled as the cure started dispersing into the atmosphere. "Genophage cured, Krogan free, new beginning, for all of us." Mordin smiled as the top floor exploded, killing him instantly. Shepard watched the top floor go up in flames sadly, although he knew there was probably no other way for this to end.

...

"Thank you Shepard, thanks to you the genophage was cured, and now we can finally fight the reapers at full strength." Wrex said.

"So you'll be deploying troops now?" Shepard asked.

"Yep, I'll be deploying Krogan to Palaven immedietely, and when you're ready to hit Earth just tell me."

"Thanks Wrex, I need to be going now, good luck with organizing the clans and such."

"Haha! Make sure to kill a couple reapers for me out there, see ya Shepard!" This definitely ended on a good note, it was neat to know that Eve's actual name was Bakara, he had not expected to be told that when they were riding back in one of the tanks.

...

"Shepard, I understand that you've cured the genophage." Counciler Valern did not look pleased.

"So what? We need their help in the war."

"It's not that I didn't approve, it's just that our Dalatrass is rising a lot of trouble over it, but that's not the reason I'm here, there's something else I need to talk about."

"What is it?"

"I've found some evidence that points to Udina doing some illegal things, but it would better if we could talk in person."

"I'll get to the Citadel as soon as I can, we can discuss this there, I knew that guy was going to do something traitorous one day."

"That'll be acceptable, Valern out."

"Joker, get the Normandy to the Citadel when you can, I have a meeting with a Counciler."

"Yes Commander, setting a course now."

Shepard walked out of the war room, waiting paitently as he was scanned by the two privates that were STILL camping the door.

"Don't you two ever get tired of camping the door?" Shepard asked.

"Nah, we get to see the saviour of the Citadel on a daily basis, and with the things you do on this ship, I doubt we'll ever get bored.

"Well, I guess that's true, keep at it, you two.

"Sir yes sir!" Both of them said with uniform precision.

Shepard smiled, the banter those two talked about was either very true or very funny, it was funny to listen to them sometimes. Humor was always welcome in a desperate war, especially since the last mission was so exhausting. He didn't feel very energized, so he decided to sleep for a bit, since it would clear his head of this pounding headache, he could see Tom after that.

...

Shepard exited his quarters and entered the elevator for the crew deck, he had to talk to Tom. He arrived at the crew deck quickly, and made his way to the medbay. Tom was on his Omni-tool when he entered the room.

"Oh hey Shepard, come to check up on me?"

"Partly yes, how are you doing?"

"Well I'm ok, but it isn't fun having radiation sickness."

"I hope you get better soon, but this wasn't the only reason I came here, is your AI, Section available?" Shepard was lucky Dr. Chakwas happened to not be in the room at the moment.

"Of course, what is it you want?"

"I've come to an executive decision that we should introduce him to the crew, but of course you won't be there to talk about it, so I was just making sure that you would feel comfortable about this decision."

Tom looked surprised. "Why are you asking my permission, if you feel it's nessasry then I'm not going to stop you, just ask Section himself, here I'll link him to your Omni-tool so that he can communicate when ever he wants."

"Can't he just do that himself?"

"Well, he's an AI on a very small piece of software, so he can't do too much at a time without overloading my Omni-tool and although my Omni-tool has somewhat better processing power then yours, if he did more then three things at once he would probably overload it, so it's easier on my Omni-tool if I just link him myself, here you go, he should be able to communicate with you at any time without any significant drop in either mine or your Omni-tools performance.

 _Hello Shepard, you called?_

"I did, I was wondering if you'd be comfortable if I introduced you to the rest of the crew?" Shepard asked.

 _I believe that would be beneficial since I would be able to exchange data with the rest of the crew, yes._

"Ok, I'll arrange a meeting an-"

"Uh, Shepard we're 20 minutes from the Citadel, you might want to come up here since none of the normal channels are responding to my hails."

"I hear you Joker, I'll be up momentarily." Shepard sighed. "I swear he has the WORST possible timing, I'll introduce you later Section, duty calls." How long had he been asleep for? It felt like a quick nap, but in reality had probably slept for longer then 6 hours, which he did not intend to do.

...

"Uh Shepard the Citadel isn't responding to my hails at all, what should we do?"

"Check emergency channels, this might be one of those situations." Shepard seemed calm, although inside he had no idea what was going on and was a little worried, but he had to stay strong for everyone else.

"This is Commander Bailey, Cerberus troops have taken control of the station and C-Sec headquarters, we need immediate assistance!"

"Joker, ask Kaiden and Garrus to get to the shuttle bay with full combat gear, and get James to gear up."

"Yes sir."

...

"Do we have any idea on what's going on down there?" Kaiden asked as the shuttle disembarked from the Normandy.

"No, all we know is that Cerberus has taken the Citadel and C-Sec HQ, which is where we're going now, C-Sec is critical if we want to retake this station."

"What the hell is that Illusive bastard thinking? This doesn't do anything to help us in the war, and you told me that he apparently has 'humanity's' best interests in mind." James said, he was raring to go.

"Ask him, not me, I only worked with him because he gave me all the supplies at the time, but Tom told me that he had bugs all over the ship, including my personal bathroom, so you can bet I have a bone to pick with him."

"When I find him, I'm carving the names of all the he's killed civilians into his skull." Garrus said, he wasn't joking.

"Commander, we're entering C-Sec HQ." Cortez said.

"Open the hatch." The scene outside was chao, C-Sec defenses were getting slaughtered as Cerberus pushed forward aggressively, and Shepard could barely make out Bailey getting shot in the stomach right next to the door to C-Sec HQ.

"Let's get out there and do some damage, Garrus set up with your sniper, I want someone watching our flank, Vega, Alenko, on me." Shepard ordered.

It has hard fighting a slightly uphill battle, but Cerberus wasn't expecting another attack on their flank so that gave Shepard's squad a small advantage at the start of the skirmish.

There were a lot of Cerberus troops, and many of them tried to flank Shepard's position, and this was the exact reason why he had chosen Garrus, many of the troopers died from a single head shot, or if they had shields, an overload, followed by a head shot. James was going crazy with his grenades, throwing them at anything that looked at him funny, and Kaiden was just providing general biotic, tech and fire support for anyone that needed help.

After several minutes of combat Shepard wiped some sweat from his brow as the last trooper got shot in the head. He jogged over to Baliey, who was injured, but it fortunately wasn't life threatening.

"Bailey, are you alright?"

"Yeah, those bastards missed my heart, I'll be fine."

"Can you get us in?"

"As long as no one interrupts me with a bullet this time."

The door opened, showing a very damaged and dirty reception desk, Cerberus, no doubt. Shepard sighed, he had a lot of ground to cover.

* * *

A/N: Prepare yourselves for canon divergence next chapter...

Reviews:

 **BrotherCaptainSheperd:** Yeah, that's right, you better deny it.

 **general-joseph-dickson:** It's just going to get better, mate.

 **redcollecter:** Like I said in the author's note, prepare yourself...

(Massive SSB4 reference here if anyone gets it)


	11. Chapter 11: Priority: Citadel

Garrus had never seen Shepard this angry before. Had seen Shepard angry before, but spirits, it seemed like Shepard was absolutely crazy right now. He knew Shepard hated it when someone died under his command, or when he saw civilians get slaughtered. He probably still blamed himself for Ash's death, but now?

He was definitely losing it. He blasted through Cerberus squads like they were nothing with that Claymore heavy shotgun. He would somehow avoid all bullets that were being fired at him, while somehow managing to fire more then one shot of his Claymore before he had to reload, which was weird considering that the Claymore had to be reloaded after every single devastating shot. And since he had disruptor ammo loaded on his shotgun, most shields were broken simple because the first two pellets just destroyed any shields that came Shepard's way.

XXXXXXXXXXX

The rest of the squad struggled to even keep up with Shepard, Garrus opted to just snipe since he knew he wouldn't be catching up to Shepard any time soon. Kaiden tried his best to keep up with Shepard, but his barrier was taking too much fire, even when it was reinforced he just couldn't take the pressure like Shepard somehow managed to.

James was the only squad member that could sufficiantly provide support for Shepard from close up, since his style of fighting was extremely aggressive at best, and at worst he was just a flanker. He still had to break to cover occasionally though, because he didn't like doing it THAT aggressively. Shepard pretty much singlehandedly won the firefights they had from the Cerberus squads they encountered.

"We should be close to the executor's office now." Kaiden said as they entered the next room.

"Yeah, his room should be through that doorway at the other end of this hallway, overlooking the room."

"Let's get to it team." Shepard said as he down the hallway, only for another Cerberus squad to ambush him.

He pulled out his Claymore, shot one guy, rolled to the left and shot another guy while he was rolling, then he pulled out his Skorpion and shot two sticky bullets onto another Trooper who screamed before he exploded into a pile of red mist. And then he ducked under a swipe from the electrical baton that a centurion was wielding and grabbed the centurion's wrist which held the baton and then shot the centurion in the groin and then the head.

"If you keep going like this Shepard I think I might retire early, you destroyed them without any help from us." Garrus joked

"Well, don't count on it, we're almost there, let's keep moving."

"Stack up on the door gentlemen, I'll breach." Shepard said professionally.

"3...2...1...Breach!" Shepard shouted before opening the door and sweeping the room.

"Bailey, they got the executor, and two Salarian bodyguards."

"Any sign of the counciler?"

"Nothing yet."

"Then don't count him out yet! Tell me if you find a body but don't assume anything else."

Shepard looked out the window which had a nice view over the entire room, and he managed to see the Councillor just as he got out from under the table and de-cloaked.

"Bailey I found him, he looks relatively unharmed."

"Then get him someplace safe! We can't let Cerberus assassinate him!" Bailey shouted nervously.

Shepard looked back, only to see a Cerberus assassin standing there holding an energy blast to the Salarian's chest.

Thinking fast, Shepard broke the window and jumped down to a hostage standoff situation, and he knew this was over, 3 on 1 that assassin stood no chance.

"3 on 1 buddy, it's all over for you." Shepard said asserting himself as the dominant person in the standoff.

"No, now it's fun." He responded casually.

"Shepard, he's going to kill us all." Valern said, terrified.

"That remains to be seen."

"No! Udina, he's staging a coup, he's going to send the other Councillors right into a trap."

Leng, not wanting the Councillor to give out any more valuable information, was about to shoot the Salarian, but that's when he heard the distinct unfolding of a pistol right behind his head. He punched the Drell right in the face, but Thane had done a lot of exercising recently, and since he had been training he ignored the blow and punched Leng in the stomach before summoning a burst of biotic power and throwing Leng to the other side of the room.

Leng quickly recovered and grabbed his sword, and was about to charge at Thane, but at that moment Section did the one thing Tom had wanted to do, but couldn't since he was unconscious as the bullet in his shoulder was being removed. Section activated the virus Tom had planted on Leng's ocular implants, which blinded him and sent him writhing to the floor from the pain of his implants cutting into his skin from the implant's clamps squeezing really hard.

At that moment everyone in Shepard's squad got a message.

 _Shoot him! I've disabled his optics and made his implants cause as much pain as possible, kill him!_

Gunfire immediately erupted after that as Shepard and co. opened fire on Kai Leng, and although his shields were ridiculously strong, they couldn't take more then 2 blasts from a Claymore with disruptor rounds at close range, and that was with other people shooting at him constantly. He went down in ten seconds since his shields managed to hold for 8 of those seconds.

 _Shepard, Tom planted a trace on Leng's ocular implants, it should show a history of where he's been, that should take you right the Illusive man._

"Thank's Section, I'll retrieve the data immediately." Shepard said before uploading it to his Omni-tool.

"Another AI?" Garrus asked quizzically.

"Hey, if it isn't homicidal like the geth, but helpful like EDI, then I could care less." Vega said.

"I was about to tell you guys about him on the Normandy, but Joker interrupted me again." Shepard confessed.

Kaiden sighed. "He does have the absolute worst timing, I don't blame you Shepard."

"Enough of that for now, Valern, will you be alright?"

The Counciller looked a little awestruck, but unharmed. "Yes, I'll be fine, but I think I should come with you." He said.

"Why? You're just endangering yourself if you come with us."

"The otherCcouncil members will need a little convincing that Udina has turned to Cerberus." His logic was actually pretty sound.

"Alright, come with us, but activate your cloak at the first sign of danger, I can't risk you getting hurt."

"I will, now let's hurry."

"Bailey, get word out that Udina's trying to seize power, can you get me a lock on their location?"

"Hmm, well I- Yes! Got it, I'm sending it to your Omni-tool, get to them before Cerberus does."

"Alright people, let's move!"

Shepard easily procured a 5 man air car and start making fast progress towards the councilor's location.

"Alright, we're almost ther-" Shepard was interrupted as a Phantom jumped on to the hood of the car.

"Garrus, drive for me, I'll take care of this." Shepard said aggressively as he took out his Carnifex and opened the door mid flight to shoot the Phantom as she attempted to break the engine. She formed a biotic barrier which reinforced her shields and stop the Carnifex from doing too much damage.

Her biotic barrier held up against the Carnifex, but after the very last shot in the clip the barrier and the Phantom's shields broke. The two stared at each other for 2 seconds before Shepard realized something.

"You don't have shields." He said simply before throwing her off the car with a concussive shot.

"Is she dead?" Garrus asked.

"Yes, she's done, how close are we to the councilors?"

"We're almost to the landing pad."

They made it there very quickly, in fact, the Councillors were still traveling up the elevator when Shepard stepped out of the car.

"What do we do now?" James said.

"Let's just wait for them to get up here."

...

About 5 minutes later the three councilors ran through the door, along with Jondum Bau who was shooting several phantoms that were attempting to kill the Councillors.

"Kaiden, James cover that door! Garrus, close it as soon as you can!" Shepard shouted before providing cover to Jondum who was taking heavy fire.

"Hold that door! Protect the council!" Shepard shouted before taking cover as the Phantoms tried to shoot him with their Phase disruptors.

The firefight was a bit longer then the other ones Shepard had fought in, due to all of their enemies being Phantoms who had better shielding then Centurions and having weapons that would force him into cover a lot more due to their high damage output. Eventually they managed to drive back the Phantoms far enough inside that Garrus got close enough to door controls to jam the door shut.

"That was too close." Garrus said.

"I agree, let's try to not cut it that close again, Jondum, are you alright?"

"I will be thanks to you Commander, I'm glad you came along when you did, I'm going to assume you came to protect the councilors, correct?"

"Actually that was one of the reasons, I'm also here for.." Shepard turned around and stopped talking as soon as he saw Udina holding the rest of the council at gunpoint.

Lightning quick, Shepard drew his Carnifex, and with one well placed adrenaline fueled shot, he executed Udina on the spot.

"Thank you Shepard, but why would Udina try something like this?" Tevos asked, clearly confused by Udina's turning traitor on the spot.

"It's just as I suspected, Udina was working for Cerberus, and as soon I proved that he was a traitor, he decided to gain leverage by holding us all at gunpoint, thank you Shepard for your quick reflexes." Valern said.

"Do you have any idea why Cerberus would do this, Shepard?" The Turian Counciller asked.

Shepard shook his head. "No, I don't, but with some intel I gathered today which points to his main base, I will know soon enough, just don't tell anyone else that, I don't want the Illusive man to know."

"Thank you Commander."

...

It took several hours before things were restored to normalcy in the Citadel. Shepard and several other Spectres had to mope up the last few pockets of Cerberus that were scattered around the station, and tons of places were secured before anyone went outside their apartments or homes.

The first thing Shepard did as soon as he got back to the Normandy was sleep, it had been a long day, and he was just done.

...

Shepard awoke in a cold sweat, it was that stupid dream again with the burning child. He sighed, why did that kid keep coming back to haunt him? Yeah he felt guilty, but even Ash's death had not given him nightmares like that, had he been indoctrinated? It was definitely plausible since this seemed like the way the reapers would try and indoctrinate him, but they were already too late, he was going to end this war before they could get any real leeway besides these stupid dreams. He still wasn't sure if he actually was indoctrinated so he kept a mental note to be aware of any symptoms, like hearing voices.

He got on his dress blues and sent the elevator down to the crew deck, he needed coffee, even though he hated the stuff, it was a more healthy way to get him up in the morning then by using a stim.

XXXXXXXXXXXXXXXX

It wasn't an enjoyable thing, doing surgery on someone, but she had signed up for it as a trauma surgeon, so these things needed to be done. Fortunately, being good at your job had perks, mainly being able to get it done faster than others in your area of expertise. Dr. Chakwas was no stranger to surgery, as she had done it many times, mainly on humans, but she could boast that she had fixed some aliens, but that wasn't her style, everyone was already thanking her for the work she did, so why rub it in?

She smiled in relief when she finally took that bullet out of Tom, and like she suspected it was an old sledgehammer round, bigger then most mass accelerator rounds, it was much easier to take out then most conventional ammunition due to it's large size. Now all she had to do was let the machines do their work in stitching up the hole.

And Shepard arrived, of course. He had a habit of doing this after all.

"Hello Shepard, have you come to check in on Tom again?"

"Yes, how is he doing?"

"I've just finished my surgery, he should be fit for duty again in one galactic standard day if no complications arise, and I doubt any will at this stage."

"That's good, I have on other thing I would like to talk about."

"Is it about Tom's AI?" That statement hit Shepard like a stack of bricks. "You know about Section?"

"Well, his Omni-tool kept firing up while he was asleep, and I decided to investigate, I must say he is a lot more factual then EDI, but I guess that comes with the cost of no dry humor."

"Many studies show that organics enjoy humor significantly more then they enjoy a factual and no nonsense attitude, Dr. Chakwas. I was simply trying to 'fit in' to make the crew feel more at ease."

"And I must say you did a good job EDI, although it is interesting to see the difference between two AI's."

"Well, I guess I'm glad this was settled peacefully, and without my intervention, I swear I'm going to have to be there for every diplomatic meeting ever after this, it seems like I'm the only one in this bloody galaxy that can solve disputes peacefully."

"Well, since both Legion and EDI were much more peaceful then what the galaxy thinks I've always decided to give an AI a chance before instantly shooting them up."

"Glad to see you have that sorted out, I'll be on my way, ask me if you need anything."

"Commander."

Shepard decided to introduce Section to Joker first just to get him out of the way, because he didn't want Joker to make assumptions because of the rumors that traveled around the ship at light speed somehow.

"Commander you've got a private message from the council at your private terminal." Specialist Traynor said.

"Right." Shepard said, and checked the message.

* * *

Dear Commander Shepard

Due to your exemplary performance protecting me and my fellow Councillors from Udina and Cerberus, we've decided to reward you with three Spectre grade weapons. These are free and shipping to the Normandy is pending.

-Councilor Tevos

The weapons are:

The Black Widow

M-11 Wraith

M-77 Paladin

* * *

That message made Shepard's day.

* * *

A/N: Hope you enjoyed this chapter, this is the part in my story where it gets significantly AU, so prepare yourself for that. Also, Cerberus is going to burn soon.

Reviews:

 **BrotherCaptainSheperd:** Even as a full paragon, I must agree, Cerberus has to burn in hell.


	12. Chapter 12: Recovery

"So now we have an AI that acts like I thought it would realistically, how many more digital friends are you going to make?" Garrus asked in a joking manner

"I don't know how many more, and what is your idea of a typical AI?" Shepard asked.

"Not extremely innocent like Legion, and not having dry humor like EDI, I thought a typical AI would be precise, punctual, and maybe a little genocidal? At least that's what I thought until I met EDI for the first time."

"Yeah, well I guess I can relate, honestly I have no idea how the hell Section actually manages to compute on just one Omni-tool."

 _Actually now that Tom has linked me with several of you I've been drawing approximately 15% of processing power from each of you, but in return I've optimized all of your Omni-tools by 50%._

"Well I guess that helps, how much can you do at one time?"

 _Before I was limited to doing one big calculation, or two small ones, but now I can do three or four bigger calculations without a significant drop in performance from any Omni-tool I've been linked to. Along with several improvements to my own code, I take up less memory then I used to, I attempt to optimize everything I can, for maximum utility. However, I had to make several radical changes to Tom's Omni-tool to improve performance. The geth upgrades he installed helped significantly._

"Tom mentioned this before, back when Cerberus controlled the ship, he didn't really elaborate on what it could do, mind if you tell me?"

 _The programming upgrades he installed gave his Omni-tool significantly better processing power then any know model of the Omni-tool to date, it's a prototype of the software Geth Prime's use in their Omni-tool, which is of course much better then anything credits could buy you on the market._

"So that's why his Omni-tool is blue..." Garrus said.

"So what else does that give him besides better processing power?"

 _Besides better processing and memory, it has twice as much storage and RAM as a normal Omni-tool, it's easier to modify, and can hack things significantly faster then a normal Omni-tool, but I can hack anything faster then his Omni-tool anyway, rendering that feature useless unless I'm somehow unavailable. The last time he's modified this Omni-tool was the day the reapers hit Earth, barring my creation of course._

Shepard sighed. "Why the hell does every date start at the beginning of the attack on Earth? Every time it's mentioned it's like a neon sign is just floating above me, broadcasting my failure to stop the Reapers before they hit Earth."

"Shepard, stop blaming yourself." Garrus said. "It wasn't your fault, it isn't anyone's fault, you could never had expected this, even with the warning message from the beacon on Eden Prime, and besides, we're going to kick the Reapers back into the black hole they climbed out of."

"I already know you're right, but it still feels like a huge weight is on my shoulders."

"I know what'll cheer you up, come with me."

...

Garrus took Shepard to the bar where they had a bit of alcohol, this definitely remedied Shepard's guilt.

"Thanks for this, I'll always know you'll have my back, Garrus." Shepard said as he downed his final glass.

"Don't worry about it, if anyone deserves to win this thing, it's you Shepard."

"I know, I think I'll go and see Tom now since I've told everyone."

"And I better get back to my calibrations."

"When are you ever going to stop doing that? That thing's already a bloody laser, how much more accurate can you make it?"

"That would be telling."

"Sure." Shepard said in joking matter before leaving the room. He made it to the Medbay in a second.

Tom was unconscious when Shepard entered the room.

"How's he doing Doctor?"

"He's just recovering from the surgery now, and his radiation posioning has been cured, he's alright, although he will have a scar on that shoulder that I didn't bother to fix, just because I don't have the proper equipment to remove it."

"I guess it's because I was a bit of a cheap skate when it comes to the medical equipment here." Shepard joked

"Well, that positive outlook of yours has already healed your scars, so I didn't expect you to invest in it after they healed, and you wouldn't have had any use of it anyway, since scars are only a cosmetic issue, they don't actually effect a person's health."

"Thanks Doc, inform me when he wakes up."

"Commander."

...

"Joker, how close are we to the coordinates the Quarians provided?"

"We'll be there in an hour, I sure hope no one picks up a contagion in the mean time."

"You know Tali would probably punch that brittle face of yours if she heard that comment right?"

"Well, as long as she isn't here I can make as many insulting jokes as you want."

"I don't know, I might slip up and mention it if you continue."

"I'll pay you 50 credits not do that, sir."

Shepard chuckled. "Keep your money, I wasn't going to anyway, but watch out for Garrus."

"Yeah, I'll do that, I sure hope Tali doesn't break out that shotgun if she hears about this."

Shepard chuckled again, Tali loved that Geth shotgun.

"Please inform me when we arrived."

"Yes Sir."

...

"How was your sleep, Tom?"

"Better then the first time I was in this bed, speaking of which, can I get off here now? It feels like I've been glued to it the entire time I've been sitting here."

"That sounds just like Shepard, you're obviously in good health now, you're free to go."

"Thanks Doc."

"Just doing my duty."

He bumped into Shepard on the elevator.

"There you are, I was about to check up on you." Shepard said.

"Well, you can stop now, I'm going to get back to my terminal in the war room now, you know me and computers."

"I told the crew about Section so don't worry about keeping him a secret, Joker is still convinced that Section is hitting on EDI for what ever reason, apparently he thinks exchanging data is sexual...?"

Of course EDI had to chime in. "I do not harbor any attraction towards Section although it is convient to meet another AI that is somewhat similar to myself, Joker is still the organic I am primarily concerned about when it comes to that matter."

Joker also decided to talk on the intercom as well. "Uh, Shepard we've approached the coordinates and a Quarian ship is hailing us, what should we do?"

"Open a channel, and tell them I'll be there momentarily." Shepard pressed the button for the CIC, Tom was with him.

"I guess duty calls huh?"

"It does, I'm probably going to have to forge an alliance between the Quarians and the Geth, just another day in the office I guess."

"I know you'll get it done, I'll be in the war room if you need anything."

...

This next bit was going to be interesting. Tom had saved Rael'Zorah, which wasn't possible in the original trilogy, so he had absolutely no data on how this would play out, nor any future knowledge, the knowledge he already had was more then enough though, so he wasn't worried.

XXXXXXXXXXXXXX

"Commander, you better get to the airlock to greet our new guests." Joker said.

"You're not my CO Joker, I know what I'm doing."

"Yeah yeah, I get it." Joker said, eyes rolling.

"Also, EDI you again have to pretend that you're a simple VI to protect yourself, since the Quarians are a little bias in terms of AI, inform everyone else on the ship as quickly as you can, and seal the door to the pilot seat so that they can't see you there either."

"Yes Commander."

"Do it quickly, the airlock is being pressurized now."

EDI quickly got the message out just as the admirals stepped out of the airlock.

XXXXXXXXXXXXXXXX

"Are the admirals on the ship now?" Tom asked.

"Yes they are, they're moving to the war room, I've got to stop talking now."

"I hear you, I'll take care of it from now on."

Shepard came in first, of course, on schedule.

"Are the admirals coming?" Tom asked, getting up from his terminal to meet Shepard who was looking at the war asset menu.

He was about to say something but was interrupted by Admiral Raan.

"As I said before Shepard, it's a pleasure to see you again, I just wish we could've met under better circumstances."

"I heard about your galactic recall, what's going on with you people?"

"17 days ago, with precision strikes against 4 geth systems, our people have began the war to take back our home world." Admiral Han'Gerrel said.

"Which was a clear violation with our treaty to the council to avoid provoking the Geth." Admiral Koris did not seem pleased.

"A treaty violation is nothing compared to reclaiming our home world and advanced AI technology." Admiral Daro'Xen said dismissively.

"We should've done this earlier, but now we're in trouble because the Reapers have stopped us." Admiral Rael'Zorah said.

"What happened?" Shepard inquired.

"We were pushing the Geth back to the home world when a Reaper signal started transmitting from this heavily armed Geth dreadnought, it can outgun anything we have and has heavy armor and shields." Rael'Zorah said, gesturing to the ship on the screen in the war room.

"That's definitely a Reaper signal."

"Under Reaper control the Geth are twice as effective as before, we need that signal offline." Zorah said, it was a statement, not a question.

"So I'm assuming you need me to take out that signal?"

"Yes Commander, we need you to infiltrate the Geth dreadnought and cut that signal using any means necessary." Raan said.

"My daughter will help you hack your way through." Zorah said, and of course Tali came into the room right at that moment, Tom had always wondered if the Admirals have planned this on purpose, as it seemed pretty well scripted.

"Tali'Zorah vas Normandy reporting for duty." She said, she seemed to be trying to be as business like as possible, probably due to her father being in the same room as she was.

"Tali, glad to have you aboard." Shepard turned to face the Admirals. "I'll ready a team to hit that dreadnought."

The meeting seemed to reach an unanimous end as the Admirals dispersed.

Tali motioned and both her and Shepard left the war room for a private talk.

XXXXXXXXXXXX

"So how's it like being back with the fleet, and your father again?" I asked.

"It's been fine, I just wish we could've avoided this stupid war."

"I thought you might have support this, you did want to see the home world again after all."

"Honestly, after talking with Legion I thought there might have been a chance for peace, but I guess the Admirals decided that war was apparently the 'best option' everyone knows that's a lie, and I'm sure my father mentioned that this wasn't the time either."

"He did, I have to say the he's right, if you had done this before the Reapers attacked, then you might have already been occupying your home world right now."

"Honestly I have a lot of worries over this, but enough about me." She changed the subject. "Who's on the Normandy now? I didn't see any of the crew members from the original Normandy, not even Joker."

"Well, Garrus is still here."

"Is he still calibrating that gun?"

I rolled my eyes. "Yes, sometimes I wonder how in-accurate that gun would be without him." He went on. "Kaiden is back, we got over the whole Cerberus thing, so don't worry about." Tali nodded.

"I've got an Arms Master down in engineering, his name's James Vega, he'll probably give you a nickname, he tends to do that for everyone. We've got Liara in Miranda's old office, she's set up here information network down there as well, so don't be surprised if she's super busy when or if you come for a visit."

"I guess she's lost here innocence now, but so have I."

Shepard smiled sadly. "It was nice to see both of you innocent at one point, it's a shame the indoctrination of her mother shattered her innocence, and it's also a shame that you had to grow up in the 2 years I was gone for, you two were like little sisters." Tali nodded, from the little Shepard could make out of her face, she also seemed a little sad by that.

"Oh, and EDI is still here of course, I-"

"I already saw her new body, it was interesting, to say the least."

I let out a breath I wasn't holding. "That simplifies things, I'm glad you didn't freak out or anything like that, it would've complicated things."

"That was why I wasn't with your for that meeting, I was just talking to EDI for a bit, although my father introduced me in such a smooth way, that I swear the it might have been planned."

"And I almost forgot to tell you, Fisher is on the Normandy, although it was such a suspicious convince that he met up with us at that time..."

"I saw him in the war room, is he alright?"

"He actually almost died once, but we patched him up, he actually just got out of the prison that is the Medbay."

"Can you call him out here? I don't feel like I want my father watching my every move in that room."

"Yeah, Joker, you heard that?"

"Yes Commander, I'll get him out of there in a sec."

XXXXXXXXXXXXXXXXXXX

...

Just before Tali said anything, Tom quickly sealed the room from EDI's surveillance, the AI would notice, in about 15 minutes. "Is any of this expected, do you know what's going to happen?" Tali was afraid, and Tom could tell. "You know I missed you, you bosh'tet, I was worried about you, and here you are, knowing the future and all that, you know my reaction to all of this, don't you?"

Tom sighed. "Look, some of this was much different, your father is dead in the future I saw, and you filled in his spot on the Admiralty board, and plus I myself wasn't in the timeline I saw, so I'm an unknown variable here, so none of this is predictable, I-"

"Alenko, Fisher, and Tali Zorah please suit up and head down to the shuttle bay, we're raiding a dreadnought." Shepard announced over the intercom.

"I'll tell you more about this later, all I have to say is this next mission will be a success, but in a different way then both you and probably myself will expect."

* * *

A/N: Shepard is in a romantic relationship with someone as well as Tom, but I'm not at liberty to spoil it until she shows up. The posting of Chapters may slow down as I have final exams coming up.

Reviews:

 **Br2nd66:** So you don't care if they live or die right?

 **redcollector:** I have big plans for the ending of this story.

 **BrotherCaptainSheperd:** I also am questioning why they just randomly decide to switch sides in ME2 to ME3, since I think (don't quote me on this) that the Illusive Man is indoctrinated prior to the first game.

 **general-joseph-dickson:** To be honest, the weapons from the Spectre terminal in ME3 are massively overpriced, and since the Shepard in this story is a Solider and is saving the bloody galaxy I figured he deserved all three of them.


	13. Chapter 13: Priority: Geth Dreadnought

There was no conversation as the elevator went down. Tali was in strange state of being worried and also reassured at the same time. She knew that Tom knew what was going to happen, be she was afraid of what he said just before Shepard called them down.

 _I'll tell you more about this later, all I have to say is this next mission will be a success, but in a different way then both you and **probably I will expect.**_

Tom knew it too, he saw her wringing her hands in a nervous fashion, something she tended to do when she was uncertain or nervous. Fortuntely the worries dispersed when Kaiden stepped onto the elevator, he had that effect on people, which was something Tom noticed was not mentioned in the game.

"Oh hello Tali, how are you doing?" He greeted warmly.

"It's good to see you again Kaiden, I'm glad your here, it's reassuring to have some of the old crew back."

"Yeah, it's good to see you too, with Shepard leading us, I know that he'll win this thing just like he did with Saren."

"I hope so." There was a hint of uncertainty in her voice.

The elevator doors opened, showing Shepard inside the shuttle.

"Gentlemen, Tali, let's be off." Shepard said courteously.

Tom was a little afraid when the shuttle flew off right into an open war zone between the Quarians and the Geth, and even knowing the future wasn't comforting enough knowing you could be shot at any moment, but fortunately, the Geth didn't use windows, ever, and with the shuttles thermal emissions hidden, they were invisible to the Geth.

"Here's the deal people." Shepard sealed his N7 helmet. "I'm going in through a damaged docking tube alone so that I can infiltrate the base and let you guys in, just wait for me to open the doors when you get to your docking port, got it?" There was the nodding of heads all around.

"Good, also make sure you have full survival gear in since you'll be in open space for a little while, and since Geth ships don't require much Oxygen or gravity."

...

"I never really was a fan of zero gravity." Tom said as he hung on to one of the handles attached to the tiny platform that served as the entry walkway.

"I must admit, it's a bit disorientating." Kaiden said.

"I've had to do it a lot." Tali didn't seem to care. "It honestly isn't a big deal, especially since we won't be here for longer then 10 minutes, when you're out in zero gravity for more then 60 minutes, then it really starts to get really uncomfortable."

The door's entry button turned green. "Heads up!" Kaiden shouted.

"I've unlocked the air lock, can you guys get inside? I'd rather not solo the Dreadnought." Shepard's tone held a hint of amusement.

"Just being honest here, you probably could, pretty sure you wouldn't want to rob everyone of the exp though." Tom said.

"I'd rather not try it, but thanks for the vote of confidence, I appreciate it." He was being genuine.

Tom felt so much better being able to put his feet on solid ground again, it was disorientating being in zero gravity for too long, now he remembered why he didn't every want to be an astronaut back when he was actually born.

"I'l glad you're all here, it was getting a little creepy being alone, Tali, can you get us through this locked door?"

"Of course, while you wait, check out Admiral Xen's prototype." Tali said, putting the weapon down near Shepard.

"Hmm, seems like a scaled down Arc Projector, I like it, does it still have the laser?" Shepard knew his weapons, he was solider after all.

"No, to save power it uses a non visible laser, but it also only requires a thermal clip for ammo."

Shepard nodded appreciatively. "Nice."

"We're through Shepard."

"Ok, let's move."

...

"So what are we looking for?" Shepard asked.

"We're looking for the control center, I can disable the reaper signal there."

"Wouldn't any access console do? I mean the Geth are networked right?"

"Shepard, that's actually a bad idea." Tom said.

"Why?"

"Sure, the Geth are networked, so your point of being able to hack any access console would work, if the Geth didn't have any failsafes in place." He took a breath. "There's too many ways that they could counter us from a regular console, that's why we need to get to the main control panel to gain administrator access, or what ever passes for control over the network."

"What ever he said." Tali said.

"Where's the control center anyway?"

"Pass a defense network and through a sensor cluster, it shouldn't be too far from where we are."

...

"Heads up, people! We've got enemy Geth units right over there, everyone engage! Tom I need you on Over-watch with that Sniper rifle."

"You can count on me, Commander." Sniping was easy and low risk, although it was annoying since some Geth just didn't stop moving, Tom was glad he didn't have to fight any Geth Hoppers, since those things were more slippery than a wet bar of soap.

It was a fairly quick fight, although it was somewhat noticeable that the Geth here were a little better at tactics then they were when Shepard was with Cerberus, at least from what Tom could remember, this was probably due to the Reaper code upgrades they had, but it barely mattered in the long run since Shepard was always better then they were, plus he was packing heat.

"Keep advancing, let's get to the control center before they box us in and form a defensive line." Shepard said.

...

"The operations center is just behind this door."

"Good, lets disable the reaper signal get your fleet to safety."

Inside the entire squad could see the other end of the room, where a Geth hunter cloaked.

"Hunters! Everybody watch your flank! Tali get your defense drone up!" Shepard snapped out before pulling out a Shotgun and shooting a Hunter who had just de-cloaked in the face.

The firefight was tough, considering Tom hated close quarters combat, his only saving grace were his Omni-blades which he used after overloading the shields since a close quarters fight with a cloaked combatant would go bad real quick, especially since Tom was terrible at melee anyway, his Omni-blades just did all the work for him, his technique was pretty bad.

"Good work team, now let-" He was cut off by the distinct sound of something de-cloaking behind him, Shepard spun around, only to see the Hunter have an Omni-blade stabbed right through it's flashlight head.

"You'll thank me later, continue with your speech." Tom said as he de-cloaked.

"Now, as I was saying before I was rudely interrupted by a Geth, let's disable that signal that's controlling these guys."

"I'm on it Shepard." Tali said before tapping several commands into the center console of the operations center, then she did the Quarian equivalent of a groan.

"What is it?"

"The Geth have blocked us from shutting down the Reaper signal here, we can't stop it from here, it's in the drive core, we can shut it down from there." Tali said.

"That should be simple enough, let's move."

"That isn't going to be possible Shepard." Shepard turned around as Tom tapped several things on his Omni-tool. "The Geth have sealed emergency bulkheads to block us off, and we don't have explosives to get all the way to the drive core. Although we could use the main battery, it can't be blocked by bulkheads and runs the length of the ship." Tom said.

"Good idea, but we're locked in this room." Tali said.

"I have an idea, Tali which door leads us to the main battery?"

"The one on the far side of the room on the left, why?"

Shepard pulled out several high explosives, they looked somewhat similar to the demolition charges used on Haestrom. Tom could almost see the grin Shepard had on this face as he planted the charges on the doorway.

"There's going to be hostile Geth on the other side of these doors Shepard, I think we should get into defensive positions."

"You're right, everyone back to the command console, we're going to need the high ground in this engagement."

...

"We're almost to the main battery, shouldn't be too much longer."

"I'm actually surprised your father let you go on this mission Tali, wouldn't he be more reluctant?"

"You obviously don't know my father very well, he loves me, and I love him, but we both know that our duty to our people comes first, although I do wish he would spend more time with me sometimes."

"You're lucky you even have an alive father, my father died when I was very young, I can barely remember him anymore." This actually wasn't a lie.

"What happened?" Shepard asked.

Tom shuddered. "I don't want to talk about it, let's just keep going, I'd rather keep my past buried, there's too many old wounds I'd rather not squeeze lemon juice on." He was being honest with that too, plus the guilt would rise up in him every time he remembered how many security systems he had hacked and given to organizations with probably nefarious intentions. He was so dead back then, he just did what his body willed, he never thought about the consequences of his actions, at least until that final hack that he had never completed.

...

"Shepard? This is Admiral Rann." She sounded distraught.

"What is it?"

"The heavy fleet is collapsing, you have to get that signal offline as soon as you can." She said urgently.

"I'll have it offline momentarily, we're almost to the source of the signal and we'll shut it down from there."

"Thank you Commander." She cut comms.

The next room was very linear, it just seemed like a very over-sized hallway, and then Tom flinched. This was THAT room, the annoying one that had the EM pulse that forced you into cover every few seconds, it was annoying as hell and he could remember that it caused him more then his fair share of game over screens.

"Watch the shockwave! That's a huge gun!" Shepard shouted before diving into cover to avoid another pulse.

"If we stick to cover we should be fine, but don't break cover if you hear it charging up!" Tom shouted before sniping a Geth rocket trooper in the shoulder.

The battle was much longer then any conventional fight, because the fight would stop every few seconds because everyone would dive into cover to avoid the blast, even the Geth weren't safe and most of them were hit at least once due to the blast always hitting them on their mostly exposed side.

...

"Bloody hell." Tom muttered as he gunned down the last Geth trooper with his Mattock, and then immediately having to take cover because of the pulse.

"Alright people, let's keep moving, we're probably getting close to the core now." Shepard commanded.

"I'm enabling the maintenance lock on this cannon, it should shut it down for a while, which should let us pass."

"Alright, let's move team."

They got about a quarter of a way through the gun before it turned back on.

"The gun's online! We have to get the hell out of here, now!" Tom shouted before sprinting like mad.

"Everyone out! Go Go!" Shepard shouted, and as soon as everyone was out, he dove and barely made it outside.

"That was a little too close for comfort." Tom observed.

"Fortunately I don't plan on walking through a cannon like that again, nor do I have a death wish so I doubt that'll happen again." Shepard said. "Okay, keep moving forward, and stick to cover when that pulse strikes again."

The next firefight was markedly faster than the previous one, due to the squad actually having experience with the pulse and knowing when to peek and when to keep your head down, it was still annoying to have your shields constantly decimated once every single Geth solider was dead though.

"We seriously need to get rid of this pulse, I'm annoyed with it disabling everything we have every 5 seconds." Tom said, his tone was laced with irritation.

"I agree, Tali can you shut that bloody pulse off?" Shepard asked.

"I think I can, give me a second to hack into this console." Tali said, she had the pulse down quickly, which was a major relief.

"Thanks Tali, now let's get to the core, everyone forward." Then of course the next door was locked.

"Great, Tom can you get Section to break this door open quickly? We're in a bit of hurry here and it would take too longer for anyone else to do it."

"I've got it, give me literally 5 seconds." The door open after that without anymore resistance.

"What's this about? Who's Section?" Tali was clearly confused.

Tom brushed her off. "Trust me, we don't have time right now, I'll explain when we're back on the Normandy."

"Ladies and gentlemen, welcome to another elevator ride, let's hope this one isn't as slow as the last one." Shepard said, sarcasm dripping from his mouth, he obviously was not happy with another elevator ride as everyone got on.

"I miss our elevator conversations." Kaiden said somberly.

"It was so much simpler back then, I wish it was still like old times." Tali said.

"Guess everything can't be as simple as chasing Saren was, those were the good days." Shepard said, forlorn.

Tom wasn't listening however, while they were thinking about their own past Tom was remembering his own, the guilt was crushing him right now, only now was he realizing how many terrorist organizations he had probably given the edge to, the guilt was like a ten ton weight, weighing down on his shoulders like he still had that gunshot wound and it was tearing his shoulder apart.

"Tom are you there? Tom!" Shepard shouted.

"Oh what I-" He looked around, everyone was giving him the look. "Sorry." He sighed. "I was just thinking about my past, I'll stop now, no point harping on what's done and gone anyway."

"Yeah." Shepard sounded uncertain. "We're at the core right now, stay alert Tom, now move out!"

* * *

A/N: After the next chapter I post I won't be able to post for a while due to my final exams coming up, so you get one more chapter before summer break, and maybe another if I get lucky and manage to squeeze in enough time to make a second chapter, but don't count on it. I feel that the pace of the story is moving along nicely, but that's enough of my rambling. I hope you enjoy this chapter, and remember, reviews are always welcome, no matter the criticism.

Speaking of which...

 **general-joseph-dickson:** I'm legitimately curious of what you think, unfortunately it probably isn't going to play out like that.

 **redcollector:** Personally I hated the part with that pulse that disabled the shields, but seeing Legion again made up for it. A lot of things will change in the next chapter.

 **Br2nd66:** What's sad about what your saying is the fact that it's so true that they drop their morality so fast that it literally makes me question how the hell the Illusive man thinks he isn't indoctrinated, although I was distracted from that by my sadness of Kaiden getting his crap kicked in at Mars.

 **BrotherCaptainSheperd:** Yeah, he was indoctrinated before the first game, at least he managed to bring Shepard back to life and help kill the collectors until he switched sides, I think what happened is the stuff they got from blown up Collector base (Reaper heart) was the nail in the coffin that really indoctrinated everyone in Cerberus, but don't quote me on that, this is supported even more if Shepard decides not to destroy the base. (Reaper brain)


	14. Chapter 14: Thinking too hard

"That's definitely Reaper tech, I can see why we couldn't shut it down remotely, but what-" Shepard was cut off as the machine reveal Legion to be tied up to several cables, all of which looked extremely resilient.

"Shepard-Commander, help us."

"Legion..." Shepard said.

"Well, I guess it's good I get to see you again Legion, now how the hell are we supposed to get you outta there?" Tom wasn't internally surprised, but of course had to act it out externally.

"Hold on guys, Legion is broadcasting the signal, how do we know that Legion isn't working for the Reapers?" Tali asked cautiously.

"Your concern is valid, Creator-Tali, however we are not controlled by the Old machines, instead, we are being used as a conduit to broadcast the command signal to all Geth platforms. We must admit that we never agreed with the Consensus when the decision was presented." He seemed almost...sheepish for an AI.

"Alright Legion, we'll get you out of there, hold on." Shepard said before activating his Omni-blade.

Legion 'flinched' when this happened. "That will not be possible Shepard-Commander, besides physical restraints, this platform also has several hardware blocks in place that would prevent it's imput from being accepted by the vessel once freed, you must free me by accessing the console on the far side of the room."

"Won't it need to be hacked? I mean you guys have tons of security measures as far as I see, or at least if Tom is right."

"We protected our consoles from remote hacking attempts, not physical removal, you should have no issues freeing us once you interact with the console.

"Tom, stay here with Legion while the rest of the squad gets to the access console, just so that he doesn't try anything, and so that nothing happens to him while we happen to be on the other side of the room."

Tom nodded. "You got it, boss man."

Just as expected, Shepard made to the other end of the room and released Legion without any trouble.

Shepard hastily tapped a couple controls on the console. "Got it, you should be free now Legion."

"Hardware blocks removed, thank you Shepard, we are free." Legion said with as much gratitude as a synthetic could muster in one voice without having any emotion.

"Tali to fleet, the signal is about to come offline."

"Thank you Tali, you've done the migrant fleet proud, I'll be the first to congratulate you when you get back."

"Thanks dad, we're getting out of here now."

That's just when Legion disabled the guns and barriers of the Geth dreadnought, leaving it vulnerable. "As a gesture of cooperation, we have disabled this ship, all weapons and barriers offline."

"Ok, now let's get the hell outta here people!" Then the Geth units started dropping in.

"Alert! Geth reinforcements incoming!"

"We'll handle them, procure an escape vessel or something similar while we kill these things."

"Acknowledged, Ghost-Infiltrator, are you coming?" Tom jumped down to Legion's level.

"Right behind you." He took out his Widow. "Since I believe you have an affinity for this thing, take it off me for this mission, I've got a Mattock so don't worry about me."

"Acknowledged, the docking bay is through several hallways, follow us."

They only started moving when an explosion rocked the ship."

"What was that?" Tom asked frantically, although this was all an act as he knew what was going to happen.

"Creator vessels are firing on this ship, we must hasten our travel to the Docking bay, Geth have no escape pods so we'll procure a fighter and pilot it to safety."

"I gotcha, I'll alert Shepard while we move." He accessed comms. "Shepard! Geth don't have escape pods, but Legion's going to pilot a fighter to safety with us in it, after you've dealt with those Geth meet up with us in the docking bay, get Tali to trace me if you have trouble finding us."

"Copy that Fisher, we'll be there soon."

 _Meanwhile_

"Continue firing upon that Dreadnought! We've have it down soon Heavy fleet!" Han'Gerrel was definitely giddy about this, meanwhile Shepard had just shot the last Geth Prime. He had heard every word on the comm, he made a mental note to make Gerrel pay for this afterwards.

"We have to get out of here people, let's quickly get to the docking bay before they destroy this ship, Han'Gerrel is going to pay for this after we get out of here, now let's move people!"

The bickering with the Admirals only got even more colourful as they made their way to the docking bay. "Hold fire you bosh'tet! That's my daughter you're firing on and I didn't promise her a house on the homeworld for nothing! HOLD YOUR FIRE!"

"Belay that order, keep firing!" They had almost destroyed the Dreadnought, fortunately for Shepard, him and his team had just reached the docking bay.

"Shepard-Commander, we've located transportation, please enter this vessel so that we can pilot to safety." There were several explosions and a disorienting loss of gravity, but Shepard and co. managed to make it to the Geth fighter which Legion and Tom were in.

"We're in Legion, thanks for the ride."

"Does the storage compartment have adequate room, Shepard-Commander?"

"Thanks for the concern, but I think we have bigger things to worry about, let's just get the hell outta of here before they blast this ship to pieces."

...

"That was a little too close for comfort, was Han'Gerrel really willing to sacrifice us just so he could destroy that Dreadnought?" Tom said the last part of the sentence with a very terrified tone, even though he knew wasn't in any real danger, although there was difference between being there in person and knowing of it, but not experiencing it, and just knowing it and seeing it.

"Yes he was, and I'll be having a little chat with him later, I do NOT tolerate anyone who purposely endangers my crew just so he can get something he wants, he's going to pay for this." Shepard's tone was laced with anger, he cared about his crew.

"This is actually insane, even for Han'Gerrel, he's friends with my father, but I'm sure that after this it'll be 'he was' friends with my father, I just hope this don't end with an Admiral being charged for treason as that would start and uproar among the people that support Han'Gerrel."

...

"So who is Section?" Tali asked.

"He's an AI I created on accident, although he's not evil or anything like that, he's actually saved my life once now."

"Really? So how did you create him?"

"It was on accident like I said earlier, I was just trying to create a simple VI, and then Cerberus corrupted my Omni-tool, and then Section decides to come along and fix everything, and now my Omni-tool is a lot better then it was before, now because I have an AI living on the thing.

"How does that work? Doesn't he take up a lot of space?"

"He's actually optimized my Omni-tool enough to the point of it being manageable, so it's not a significant drop in performance, although my Omni-tool does get a little laggy when he's thinking too hard.

 _That was only twice! And I was computing how the emotions of organics are driven, so you can't say it's a habit._

"And there he is, he's a bit more factual then EDI, but he doesn't have nearly as much humor either, so that's basically how I got Section in a nutshell, also he's recursively self improving himself all the time.

"When I first heard of EDI on the SR-2 I was a little scared, mainly because I thought she would turn on us, especially when she became unshackled, but she has proven herself time and time again, so now I guess you could say I'm a little more comfortable with AI? I'm a little less insecure around them now, especially with both EDI and Legion running around with a body."

"Oh, and before I forget, Han'Gerrel is probably getting chewed out badly by both your father and Shepard.."

 _Meanwhile_

"With all due respect, _Admiral_ your uni-lateral strike endangered not only but your own fleet, but the safety of my squad as well, get the hell off my ship, and don't ever come back!" Shepard said angrily. Gerrel retreated like a hurt puppy quickly after that.

"Shepard I know you're angry but..." Admiral Raan tried to placate Shepard, but she was cut off by Tali's father.

"No, Shepard's anger is justly incurred, Han'Gerrel was being reckless, and I believe Shepard's anger was him protecting his crew." Rael'Zorah said, clearly supportive of Shepard and why he had just kicked an Admiral off his ship.

"Shepard-Commander, we are prepared to offer assistance." Legion came in at just the right time.

"What the hell is this?! Commander? Commander!" Raan shouted.

"Oh that? That's Legion, he helped me fight the Collector's and kill the Heratics, and if you want to study it Xen, I believe you can join Gerrel in getting the hell off my ship, as I won't stand for that right now." Shepard took a breath.

Xen was very surprised at that Shepard knew that she was interested in Legion. "Wha-" She sputtered, which was very uncharacteristic to her normal cold, calm and calculating demeanor.

"I know how interested you are in the Geth, so don't be surprised when I know things that seem a little odd, you don't hide your interests very well."

"Shepard, before this Geth came on, I was about to say, thank you disabling that signal, we'll be able to retake our homeworld now that the Geth are no longer under Reaper control." Zorah didn't seem to perturbed, despite there being a live Geth in the same room as him, he was good at keeping a steady head.

"This is a false assumption, you have disabled the Reaper's short distance communication signal, their long range communication signal will be on soon and the Geth will be under Reaper control in approximately 23.53 hours in galactic standard time, we recommend a re-group and to make a defensive formation."

"Wait what?! Xen, coordinate with Gerrel, MOVE!" Zorah snapped, losing his calm after hearing that statement.

XXXXXXXXXXXXXX

"So you know what mission we're about to do next?" Tom hastily muted this part of the ship so that EDI couldn't hear anything more

"Yeah, we're either going to infiltrate a Geth base to shut down Geth fighters so that they can't target your Fleet's live ships, or we'll be rescuing Admiral Koris who crash landed his ship on the planetary defense cannon you saw in the Dreadnought to disable it. And after that Shepard will know where the Geth base is that's controlling the Reapers and immediately go for that or he'll do the other mission and then destroy the signal."

"It's always a little unnerving when you know the future and likely know a lot about myself and the rest of the crew, I'm glad you're on our side."

"You know I wasn't always a good person before this, when my parents died I was disconnected, I just did what I did best, I hacked a defense network, gave information that I hacked to the highest bidder, I only started realizing my greed just before I was transferred here, I must admit that I wasn't the greatest person, the guilt is starting to weigh on me now." Tom looked very guilty.

"Were and when were you before all of this?"

"I was on Earth, in a universe where the Reapers and none of the aliens like you or anyone else existed, at least we hadn't found any yet, and the year was 2013 and we could barely get off our own planet."

"Keelah! How did you adapt to today's computers? You're smarter than I thought."

"I worked at it for 4 months, I spent the other 4 training my body for combat, when I commit to something, I usually commit fully, that's why I was such a good learner, I had a PHD in computer science, and I self taught myself how to use a computer after my father died, I wonder how my family, or what's left of it is doing now, but that's enough about me."

XXXXXXXXXXXXXXX

The intelligence was not pleased. Well, as close it could be without showing emotion. The Shepard was undoing their work on the AI creations, the Geth. This was unacceptable, and plans would be set in motion to prevent the Shepard from completing their goal. The intelligence made sure #9845843 was aware when the Shepard launched their attack on the communications base.

There was also the Anomaly, which was something not accounted for. They were not a concern as of now, their actions would be dealt with and a contingency would be set in motion if their actions disrupted the harvest. This was not normal, but not unheard of for a contingency to be in motion, in the end, there was no war, the intelligence mused.

There was only the harvest.

XXXXXXXXXXXXXXXXXX

...

"Tali, Garrus and Tom please report to the shuttle bay for a mission on Rannoch." I said calmly. I had to make sure the civilians were safe before I started doing other things, like finding the main communications base, I couldn't let what happened to the civilians on Earth happen here, at least here I could make a difference, as opposed to where I couldn't do a bloody thing when the Reapers first attacked Earth.

There were Tali and Garrus, those two that had stuck with me the whole way. This was so much different from the old days, I'm glad these two had managed to stick with me the whole way.

"Hey you two, it's been a while since we've all been together shooting Geth huh?"

"Wouldn't have it any other way." Garrus said, his mandibles showing the Turian equivalent of a smirk. "With me here you'll be able to do it in a stylish way, so that's a plus." I had to admit that Garrus was a badass, although I would never tell him that because he wouldn't know what I would mean by that, and if he did know it would go straight to his head.

"I guess we've all grown a little over the course of the years, I miss the simple times when all we did was chase Saren, shoot large plants and kill Rachni." Tali's Thorian reference was very subtle, it was almost like an inside joke now, which only the old crew and for some reason Tom knew, I still hadn't figured out how he knew that though, and there he was, the would be enigma if he didn't treat every like old friends, and like he knew them several times over, which was slightly unnerving.

"I'm here guys, did I miss anything?"

"Just some old memories, you wouldn't have been able to relate since you weren't on the original Normandy, so don't worry about it, let's just go, we have a job to do after all, Legion's inside."

...

XXXXXXXXXXXXXXXXXXXXX

"So what's the objective here Legion? How are we going to shut down the servers? High explosives?" Shepard had that grin again, he really liked seeing things blow up, but could you blame him? If anything that would be a break from dealing with politicians.

"That is crude and inefficient." Legion seemed to chide Shepard, who deflated once he heard that. "We will disable the server internally."

"Internally, you mean we'll be infiltrating their base and disabling it like how we did with the Heratics? What we expecting for resistance?"

"Resistance is unlikely in the physical server room, it is however anticipated only within the server itself."

"What?" Shepard looked surprised. Tali shot me that look, the 'you-know-what's-about-to-happen-and-you-think-it-wasn't-good-enough-to-tell-me?!' look, at least from what I could discern from her limited facial expressions, although her body language was exaggerated enough for me to catch on, sort of. I had to give that grin, that shit eating one, and let me tell you one thing.

It was super satisfying.

* * *

A/N: To make up for me not posting next week this chapter is a little longer. I hoped that I write out how the the Reaper overlord thought, and I think I did well, but I guess that's to you, the reader to decide. Currently have my final exams next week so there will be no chapter post next week, sorry!

Reviews:

 **BrotherCaptainSheperd:** I think that's the most feasible theory as to why they switch sides so quickly in the third game, but in the end it doesn't matter. Do you want to know why? Because Shepard is going to go full Renegade on them if you know what I mean.

 **general-joseph-dickson:** You're 100% right there, and after this chapter you've probably come to this conclusion:

Tom is running out of lies and self esteem, he's going to crack soon, but that's all I'm at liberty to say right now.


	15. Chapter 15: Sentimental surge

"You're a bosh'tet Tom." Why was Tali so pissed at Tom? There just didn't seem to be a discernible reason as to why, I saw this on the shuttle too, as soon as Legion mentioned Shepard directly interfacing with the Geth collective Tali just seemed to randomly get angry at Tom. This was exceptionally rare too, as normally the two were comforting each other, it wasn't a secret that they...what was that human saying? Had a thing for each other?

"Relax Tali." Ironically Tom himself was anything but relaxed, he had beads of sweat running down his forehead, and my visor told me that his vitals were going a little bit crazy, because I'm pretty sure for humans that 120 beats per minute is a little...much. "Shepard isn't in any danger, he'll be fine, just relax." What did he mean by that? This was getting a very odd.

"What's going on? Do you two know something I don't? And Tali, why are so pissed at Tom?" I decided to cut the snark this time, this was serious.

Tom's heartbeat got even faster, now it was at 140 beats per minute, which is probably unhealthy.

"It's uhh..." His heartbeat was 155, definitely unhealthy at this point.

"You can tell him Tom, her voice was a little less pissed now, but it still held an edge to it.

"I can't anymore I-" Tom passed out.

"Tom!" Tali was terrified, I doubted she'd ever seen a human faint before except by Shepard's fist, but I knew this wasn't going to be an issue, since his heartbeat was slowly dropping, he'd passed out from shock.

"Is he going to alright, Garrus?"

"He'll be fine, you just stressed him out too much, his heartbeat was at 165 when he passed out, so that's probably the cause, and it's dropping slowly." I reassured.

 _Meanwhile_

"Is that...Tom? On his computer?"

"Yes, Shepard-Commander."

"Why is this stored in the Geth collective? I know you and him are friends and all but..."

"This event is significant to the Geth due to it being the first time when an Organic being interacted with us in a non-hostile attitude, on that computer he is looking at me for the first time, he was the one who initiated communication, we must admit that this is a litte odd considering standard human behavior.

"Why would this be considered odd?"

"We calculated that the odds of him shutting down his terminal at 4.5 seconds after seeing us were 98.44%, and his chances of initiating communication in a non hostile manner 0.1337%."

"Heh, Organics aren't know for always staying true to statistics, and don't spit out a bunch of numbers after I finish this sentence as I don't want to hear it, let's continue, we'll discuss this later."

Legion nodded. "Acknowledged."

XXXXXXXXXXXXXXXXX

"He's waking up."

"Shouldn't we help him?" Tali said, panic laced her tone.

"There's nothing we can really do, he just needs to wake up on his own."

"Okay."

"Gah, how long was I out for?" Tom rubbed his eyes as he got up.

"Around 3 minutes, are you alright?' Garrus asked.

"Yeah, I'm fine I just passed out, I've had this happen before, it's not particularly unnatural for me to faint under extreme pressure, I'm fine."

"I was worried Tom, are you sure you're okay?" Tali still seemed slightly perturbed.

"No worries I-" Tom was cut off as Shepard's pod opened and a slightly disorientated Shepard stumbled out, but he managed to catch himself before he fell.

"Well that was...interesting to say the least." Shepard said.

"Are you alright Shepard?"

"Yeah, just a little dazed from the whole thing, there wasn't really any danger though, I'm okay."

Garrus would've admitted that he was little uncertain that they were getting out of this one though, as several Primes started powering up, he knew Shepard would get them out of here alive, but there was probably going to be some casualties.

"Uh Shepard, several Primes are powering up." Garrus said, reaching for his rifle. Tali also quickly had her hands on her holstered pistol, just in case she had to draw it at a moments notice.

"We have transfered all the Geth programs from the sever in these Primes." Legion said.

"Why?!" Shepard held a tone of anger in it.

That's when all of the 'eyes' of the Primes turned blue, indicating a loss of Reaper control.

"They want...to join us."

"Well that's a relief, alright, back to the Normandy everyone!" Shepard commanded.

The one thing that stood out to Garrus through the entire mission was this one simple fact:

Tom didn't even seem slightly paranoid at all when the Primes started powering up.

...

"Thank you Shepard for disabling those Geth fighters you saved around 20% of our Live ships." Raan was very grateful.

"Don't mention it, also where's Admiral Koris and Admiral Zorah? I wanted to talk to them."

"Koris sacrificed his crashing ship while you were disabling the fighters, Admiral Zorah was on it when it went down, we got a little communication through, indicating that everyone survived the crash, but a Geth search party has been sent out to take them out." Raan sounded ever so slightly distraught.

"Give the coordinates of the crash site, I'll go and rescue them."

"Thank you Commander, I'll have the coordinates sent to your Omni-tool, good luck."

...

"Tali, Liara and James report to the shuttle bay with full gear, we're going to be rescuing two Quarian admirals."

XXXXXXXXXXXXXXXXXXX

Every time he closed his eyes he could just image all of those families destroyed by the Reapers, it was tearing him apart. Why couldn't he have just warned the Alliance? They just wouldn't believe him, especially since he was busy with other things and he didn't want to draw any attention at the time, now it had come to haunt him.

Was this PTSD? Unlikely but possible, he wasn't particularly weak mentally however, so he cast that thought aside. Maybe it was Survivors guilt, yeah, that had to be it. Out-living so many people and KNOWING about it was definitely something that he could see effecting him, this was insane.

He wished he could go back, and fix several things, regretting stuff means a lot of things, but it mostly means that no one is perfect, what a difference between machines and organics. And that's when Garrus walked in.

"Uh, hi Garrus." Tom sputtered, he wasn't expecting this.

"Hello Tom, I just wanted to talk about some things, you never finished about why Tali was so angry with you earlier, can you tell me now?" Garrus was suspicious. "And how were you so calm when Legion downloaded those Geth into the Prime units? Even Shepard was caught off guard and he was in the server."

Tom's mind raced at a million miles per minute. The gig was up, Garrus knew he was up to something suspicious, he was 100% screwed. He may as well come clean, what else could he do? There wasn't much else he could think of, and he could never take Garrus, he was bad enough at unarmed combat as is. I hastily disabled EDI's ability to monitor the room, he couldn't risk her knowing as well.

"You know Garrus, do you remember that conversation you had with Shepard? Do you remember the ruthless calculus of war?"

"How do you know about that?!"

"Oh and how is your sister doing? You're worried about her getting off Palaven safely aren't you?"

"Spirits, how do you know about all of this? Only Shepard knows those things. It's almost like you've be-"

"Been there before, and I have Garrus, that's why I wasn't terrified in the slightest when those Primes came online and why I knew about both of those conversations you've had with Shepard, and no, I wasn't monitoring either of those things. Also, do you remember that conversation you had with Ashley? In that Citadel elevator three years ago? I know that too, you want me t-"

"You've made your point, how do you know?!"

"Let's just say I was never supposed to exist here, I was transported here with knowledge of the future from a time when Humanity could barely escape Earth's orbit, I know what's going to happen, and when, I could never tell anyone, it would never make sense, let's just say I was sacrificing a billion over here to save the rest of the Galaxy, because my knowledge would be useless if I revealed everything so quickly."

"Why haven't you told Shepard about all of this then?"

"I try to do it in ways that show I don't know the future, like how Section leaked the location of main base of Cerberus, which is hidden in the Horsehead nebula. And for a second do you really think that Shepard would or anyone else would believe me? The only reason you do is because you've pieced it all together. Do you think I didn't want to tell Shepard or anyone else? No, true to be told it's tearing me up inside, I wish I could've done something to save everyone I-," Tom's voice started breaking up. "It's just I want to save the-mm all, all those families, it's all my fa-ault."

And then a bewildered Turian watched as a grown man shed tears.

...

XXXXXXXXXXXXXX

"Koris, Zorah, I'm dropping two of my squad mates down to help you stay alive while I save those civilians, okay?"

"Copy that Shepard, the help is appreciated, I doubt we'd both be able to make it out alive without your help." There was some gunshots on the other end of the line while Zorah talked.

"I hear you, transmit your coordinates and my squad members Tali and James will come to provide fire support."

"Transmitting the coordinates, please execute haste however, I don't believe the civilians will last longer then 20 minutes."

"Got it, I'll be there in 5 minutes."

...

"Everyone stay in cover! I'll take out those Geth troopers while you get to cover!" Shepard said shouted as loud as he could before opening up hellfire on the Geth troops that were advancing, fortunately there was one solider down there that providing cover as best as he could.

After several dead Geth bodies later Shepard's shuttle landed behind the cover the civilians were hiding behind. "Everyone get in here, now!" Shepard shouted as he shot a Juggernaut that was getting too close for comfort. There were no casualties as the shuttle lifted off with the Quarians in them.

"Zorah, we've got the civilians, how are you faring down there?"

"We'll be overrun soon, but we can hold position for long enough for you to get here, make haste." Zorah seemed to always have a calm presence, even while under fire.

"We're coming, hold tight."

XXXXXXXXXXXXXXX

Tali had never seen her father in action, but when she did, it was a pleasnt surprise to see him have leadership that was only slightly weaker then Shepard's.

"Cover our flank Tali! We can't have that pyro get too close!" He shouted before spraying down a Hunter that he had seen cloaked with pretty keen eyesight.

"We've got a Prime incoming!" Liara shouted before shooting the hulking Geth with her Paladin several times.

"I'll get a tactical scan on it, focus fire!"

"The calvery has arrived, we'll keep them off your backs, we'll land at your flank and keep you covered while you retreat, Shepard out."

The battle was virtually won after that since the heavy firepower Shepard was packing was a welcome assist, soon the battle was very much in their favor, and as soon as the Geth presence was decimated Shepard landed.

"Get in before reinforcements arrive, I don't plan on having any casualties, Vega how's your thigh?"

"It's fine Amigo, that Medi-gel helped out."

"Good, Cortez, get us out of here."

XXXXXXXXXXXXXXXXX

...

"Can you at least tell me how the war ends?" Garrus was a little uncomfortable, considering Tom had just finished crying and weeping, he figured the burden of knowing what was going to happen was at least enough pressure to hurt him more then anything he could do to him physically, and he'd been nothing but helpful when Shepard had recruited him, it still was a little off putting to know that he knew that his squad would've been decimated.

"Yeah, I-" Tom sniffed. "We win, but in every single ending, Shepard sacrifices his own life to kill or change the Reapers, and in every single ending I saw the Reapers are no longer a threat, the Crucible is the key."

"Is there anything else I should know?"

"Oh, there's one other thing you deserve to know, and it's that both your sister and your father make it off Palaven alive." That was some instant relief for Garrus right there.

"I think we should stop this decision now, since my counter measure which prevents EDI from listening in isn't going to last much longer without her getting suspicious."

"Thank you for tell me this, I understand that it took a lot of courage to tell me up front, although I still need to do one thing, disable your counter measure quickly." Tom complied without resisting.

And then Garrus did the one thing he had wanted to do after hearing that Tom knew the future.

He punched Tom's lights out. It wouldn't fix anything, but he got a grim satisfaction from seeing Tom unconscious.

XXXXXXXXXXXXXXXXXXXXXX

"EDI, I need you to patch me into Admiral Hackett, mark the call as urgent."

"Will do Shepard, patching him in now."

"Shepard? What's the call for? It was marked as urgent by your AI." Hackett was surprised.

"I have extremely valuable intel that could help us win the war, but I can't say anything since this channel may as well be bugged, I need you to come to my ship as soon as possible, we'll talk in my cabin there since I'm sure it's not bugged at all."

"How valuable is the intel? Why does it warrant this kind of response?"

"It could help us win the war like I said earlier sir, but if anyone else knows that we have this kind of intel it may as well be worthless."

"Very well, I'll come with my ship, where do you want to meet up?"

"I'll send the coordinates to you now, you need to know this, trust me." Shepard was absolutely certain this intel was good, considering it showed where Kai Leng had gone, and it had even had a bit of video footage which was invaluable. He could only hope the Illusive man still didn't know he had this intel.

* * *

A/N: Yeah, the plot is getting thicker and thicker, this where it all changes. Sorry for the cliffhanger, but it just seemed perfect to end it off there.

Reviews:

 **BrotherCaptainSheperd:** Eh, that seems a little too soft.

 **redcollecter:** That would be telling.

 **Pietersielie:** You're welcome, thanks for your support!

 **general-joseph-dickson:** I hope this chapter peeked your interest, because you have quite a good understanding of literature and how people communicate and such.


	16. Chapter 16: Priority: Rannoch

"Thank you sir for coming all this way. It must've been a long journey." Shepard said respectfully.

"At the very least you deserve it, Shepard. At ease, now what is it that you wanted to tell me that's so important?" Straight to the point, this was definitely Admiral Hackett.

"Sir, I have actionable intel that reveals the location of the Illusive Man's main base of operations, I know he has agents in the Alliance which is why I have you on my ship, EDI are you sure this room is secure?"

"Yes Shepard, the only listening devices in this room are my own, and I will not disclose this meeting to anyone unless told otherwise, you are my CO."

"Thanks EDI, anyway, his main base of operations is here, in the Horsehead nubula as you can see here one of my squad mates who wishes to be anonymous had a tracer on one of the Cerberus agents we encountered, and all the navigation data points to a base near a star on the other side of the Horsehead nubula." Shepard pointed towards the estimated location.

"Thank you Shepard, this data will cripple and possibly destroy Cerberus, but how are we going to do it without the Illusive man finding out? He would have contingency plans in place, and if what you said earlier is correct, the Illusive man will know in advance and will take appropriate action to prevent us from storming it."

"You know those N7 strike teams you mentioned earlier in that email? Put together an elite task force of them and send there to storm the base, you might not kill the Illusive man, but you would badly damage Cerberus and make them weaker later on."

"I'll assembly a strike force and hit Cerberus when they aren't expecting it, it'll take a while Shepard, so don't expect Cerberus to be gone immediately after this, I'll have to do several extensive background checks first, especially concerning my own crew, thank you for this information Shepard, you have given us a chance to cripple Cerberus for the rest of the war."

"Just doing my job sir, and be careful in the Alliance, Cerberus has indoctrinated spies everywhere."

...

XXXXXXXXXXXXXXX

"I probably deserved that, hell of a bruise though." Tom said as he walked in the main battery.

"That was what you deserve, I know it wouldn't change anything so I decided not to take it further then that." Garrus said, no nonsense.

"I definitely didn't expect it, but you're right and I won't be trying to get revenge because I deserved it, just making sure you don't hold a grudge."

"Normally I would, but we have bigger concerns and you've already made up for what you've done by giving us intel on the main base of Cerberus."

"I'll be giving you a lot more then that in the future, I just want to make sure that all the civilians that were killed in this war died to give everyone else a chance to end the war and keep everyone else alive. Also I was wondering wh-" The intercom suddenly cut Tom off. "EDI, Tali, and Tom get to the shuttle bay, we're retaking Rannoch today."

"What was it that you were going to say?" Garrus asked.

Tom swept it aside. "Nothing important, I have mission, I'll tell you about it later."

...

"Legion, how heavily defended is the base?" Shepard asked.

"It is recommended that you mount a frontal assualt, we will infiltrate through a side entrance and grant you a straight path to the transmitter."

"Wait, that would mean you would still have the Reapers upgrade code, right? There's no other way you'd be able to break past the security."

Legion legitimately seemed ashamed. "We feared you would disapprove, and wanted to facilitate unit cohesion."

"Just tell me next time, okay? The Geth are better than this, I'm sure of it."

Legion still looked ashamed. "Actually, base on preliminary evidence, they are not."

"We'll talk about it later, infiltrate the base while we cause a distraction."

"Acknowledged."

"Seems like you do infiltrate, mind if you could revisit your statement earlier, Legion?" Tom remarked jokingly.

 _*Flashback*_

"Security seems to have tightened a bit since my last visit here." Shepard observed.

"After the Geth attack there was a review of security protocal, some minor changes were made to reduce the risk of Geth infiltration." Wait what?! She didn't even recognize Legion as a Geth! In the game that made sense but here?! Tom turned around.

"How do you do that?"

Legion's headplates raised in a sheepish 'gesture' "Geth do not infiltrate."

"Seems like you infiltrated Citadel security, buddy, considering you haven't been shot on site yet." Shepard said, he had a smirk on his face.

"Geth do not _intentionally_ infiltrate."

"Yeah, we get it, let's go. I need to get some more weapon mods." Shepard still had that grin though.

 _*Present*_

"That was an organic complex. This is not."

"Whatever, good luck Legion!" Tom said as Legion got off and the shuttle continued on.

"Still wondering how the hell he managed to walk through the Citadel for 24 hours of shore leave and NOT get caught." Shepard said.

"Don't question it, it works better that way." Tom said.

"Shepard we're at the LZ, you ready to go?" Cortez asked.

"Oh right, yeah, everyone off!"

"Wow, I guess it hasn't really sunk in yet that I'm actually on the homeworld." Tali's tone had trace of awe in it.

"Hadn't you gotten over this when we were rescuing your dad?" Shepard said, he was poking at her, teasing her.

"Okay, that was different, you bosh'tet! I was more worried about my dad then anything else." She said, flustered.

"What ever, let's get moving."

Finding the welcoming party was easy, fighting them was not.

"Geth on your six, Tom!" Shepard shouted before spraying it a couple times with an N7 eagle.

The welcoming party was very well equipped, with hunters for pressure and a destroyer to keep them pinned down, fortunately Tom's tactical cloak managed to negate that advantage when he stuck his Omni-blade right through the destroyer's head. Shepard was taking out the hunters left and right with neat, well placed headshots, he was probably was adrenaline.

The battle was over in a couple minutes.

"Everyone alright?" A couple of nodded heads all around. "Good, we got more targets to clear, keep moving."

...

Fightning on the balcony was annoying, espically since they were always getting shot from the top floor, and being hit by hunters on the bottom floor.

"EDI! Keep an eye on those Hunters! Tom get rid of those rocket troops by any means necessary! Tali, on me!" Shepard snapped before spraying down a hunter that had gotten too close for comfort.

EDI easily cleared the remaining hunters out of the bottom floor, due to her being a synthetic and easily being able to dectect the slightest and most subtle cloaking devices.

Tali was just providing cover fire for Shepard by distracting the rocket troops with her attack drone, which were then promptly sniped by Tom. Shepard himself was shooting anything that moved, and throwing in some grenades for good measure.

"We're clear, move forward, I think we're near where the transmitter is, good work guys."

...

"Shepard, the Geth under Reaper control are closing a blast shield over the transmitter."

"How long would it take to break open?"

"7.86 hours with consistent fire from the main fleet of the Quarians."

"We don't have that kind of time, where can we disable it?"

"Sending the coordinates to your Nav point, we will disable the security and lift the blast shield after you grant us access to the console."

"Copy that, we'll proceed and disable the security from the console, hold on for a minute."

It took a while to get inside because of crossfire from the balcony on the other side of the base, mainly rocket troops, and it took a lot longer then normal because only Shepard and Tom had sniper rifles.

"Forget the sniper Tom, everybody stay in cover and get to the other side of the balcony, we're losing this fight because we don't have the appropriate amount of weapons to deal with it."

It took a while, and Tom swore he almost blew his ear drums out from all the explosions, but they eventually made it to the other side where everyone hastily entered the door and then Tali sealed it shut with her Omni-tool.

"That was annoying." Shepard remarked. "Let's keep moving, my nav point shows that we're close to the console, we're almost done, keep up the pressure."

There were no Geth inside the area, well except until after Shepard gave Legion access, then they started pouring in to attempt to stop Shepard. Of course it had to be right after they gave Legion access, how convenient.

Tom was fighting an admittedly losing battle as he was terrible at defending a location, he was much better at infiltration then anything else. Shepard was killing Geth like nobody's business, he was getting clean head shots everywhere, and he was probably running off adrenaline, again. Tali was having a much better time defending then Tom was due to having two drones which she could throw out on command. EDI was providing cover fire for Tom after running simulations that calculated Tom having a 43.5% chance of successfully holding the console, and eventually the Geth didn't have enough reinforcements to keep on attacking, so they quietly retreated.

"Shepard-Commander, I have successfully bypassed the blast shield controls and lifted it from the transmitter." Legion said.

"Good work Legion, let's get outside everyone!" Shepard shouted.

"Negative Shepard-Commander, the area behind you has been locked down, there is an elevator which will take you up to a balcony which will provide an optimal targeting position, I am marking the location your nav point."

"Alright never mind, everyone follow me!"

And just like in the games, there was a Geth Prime and two Pyros waiting for them at the lift."

"Focus fire on those Pyros! We can't have them getting close!" The Pyros were shot down like they were marked for death, and then the Prime was eventually taken down with combined fire.

...

"Primes! They really don't want us up here!" Tali ducked into cover to avoid a siege pulse.

"Flank them Tom! I need you to distract them from behind!"

"Will do Commander!"

The only reason Tom actually made it out of the pinned down position that Shepard and everyone else were at was just because of his cloak, he made a good distraction as well as two of the Primes immediately turned around once he shot one of them. It was hard dodging everything that got thrown his way, he had to holster his Mattock just to keep with the constant pulses that kept on being shot at him, any cover he took refuge in was decimated quickly.

Fortunately Shepard and co. had just finished disabling one Prime which attracted the attention of one of the other Primes, which was a welcome break. Catching his breath, Tom sighed happily, before looking up to see a siege pulse coming right for him. His shields were decimated instantly, he was about to be vaporized when Tali grabbed him and pulled him into cover.

"Thank you, I wouldn't have lasted if you hadn't pulled me in right there." He was hyperventilating.

"We're even now, let's finish off that last Prime." Tali said before switching to her Geth shotgun.

The last Prime lasted about as long as the one on the elevator, not very long.

"Alright, I'll destroy the transmitter guys, then we can go back to the Normandy." Shepard said, relief was evident in his tone as he pulled out the targeting laser.

He painted the target and the Normandy rolled in and deployed a perfect air strike, hitting the transmitter dead on.

...Only to piss off the Reaper destroyer that WAS the transmitter. Shepard fell off the balcony in the resulting shockwave.

"The transmitter is a Reaper, start running people!"

"We have located transportation!" Legion said.

"You heard the robot, everybody get your asses to the escape vehicle, NOW!"

Everyone made it to the vehicle, and then Legion hit the gas.

XXXXXXXXXXXXX

The order was issued to #9845843 in an instant.

 _Kill Shepard, extinguish the last hope for this cycle, and then continue transmitting._

Projections calculated Shepard of dying in 96.35% of all simulations, there was no escape this time, Harbinger had made it personal, they were inferior to Shepard, they had failed.

 _Finish what Harbinger started, kill Commander Shepard._

XXXXXXXXXXXXXXXX

The Reaper got up, slowly, but it got up, that shot wasn't enough to kill it, sure it had stunned it, but the damage itself was minimal.

"Shepard-Commander, we may retreat before it retaliates." Legion stated.

"No, pull over."

"Shepard-Commander?"

"If we retreat now the Geth stay under Reaper control and the Qurians are dead. Retreat to a safe distance, I'll take care of it for now, EDI, have you synced up the Guidance system to the rest of the fleet?"

"Yes Shepard, anything you paint will show up on their targeting programs as well."

"Good, I'm going in."

...

It was amazing how Shepard deftly dodged those lasers, it was crazy how he dodged death so many times, and weakened the Reaper enough to disable it, in all honestly, there was a lot more to Shepard then just his skill, although that was definitely a factor. For Tom it was very different seeing it in real life, it got his blood pumping, as he knew there was no restarts here, dying would be permanent.

Shepard didn't though, he managed to single handedly take on a Reaper and WIN, and you couldn't give the fleet too much credit as he was actually exposing himself.

"We killed a Reaper, keelah." Tali was awestruck.

"That's number 4, I better get paid overtime for this when it's all said and done." Shepard said, sweat falling down his forehead.

"We can confirm that the Geth are no longer under Reaper control, we are free."

Tom inwardly sighed, this was probably the worst part, out of all the crew members, Legion deserved it the least to be killed in the third game, he was so innocent, yet deadly.

* * *

A/N: Sorry for the cliffhanger, I just couldn't find any where else to end it, in foresight I probably should've planned this, oh well.

Reviews:

 **redcollecter:** You'll see soon enough.

 **Dickson:** I tried to cut that down in this chapter, I hope that helps.


	17. Chapter 17: Sleep it off

"I'll call off the fleet, Tali get me on a fleet wide comm, I'm going to have to yell loud enough to subdue Gerrel before he goes gung-ho on me again." Shepard said, it was sad how he considered this a menial task, as his voice betrayed that tone.

"I've got you on a ship comm Shepard, do the best you can." Tali was clearly put off by Shepard's choice to have Legion upload, but she followed him anyway.

"Hold your fire! The Geth are about to return to full strength and Gerrel, if you give the order to attack I will stand by and watch as the Geth lay you to waste, I saved your fleet several times in this past week, I stopped that dreadnought, and recently stopped the Reaper influnce over the Geth, but I'm done helping you, if you attack you'll be sealing your own fate, Shepard out, Keelah se'lai."

There was a pause. For everyone but Tom it seemed like a year, but then it happened. "All ships, hold your fire." Gerrel said, he was admittedly a little surprised by Shepard's sudden out burst.

"Copying code insufficient, direct personality dissimulation required." Legion turned to face everyone. "I'm sorry Shepard, I have to go to them, it's the only way."

"Legion, the answer to your question, was yes, you had it the entire time." Tali was moderately distraught.

"I know Tali, thank you. Keelah se'lai." Legion deactivated as all of it's programs permanently disbanded to provide all Geth with the highest level of intelligence, a true form of sentience.

"Thank you Shepard."

"Raan? How did you get here?" Shepard inquired.

"My ship crash landed not far from here, me and my entire crew are fine, thank you for stopping Gerrel, had you not stopped the Geth would have destroyed the remaining population of our species, I have no doubt about that."

"Just doing my job, I think it's time I get back to my ship, Tali are you coming?"

"Yes, I may have my homeworld back but it won't mean anything if the reapers win, I with you until the end." Tali's voiced held absolute certainty.

"Good to see you're staying with us, Cortez we need pickup."

"On my way Commander."

"Are you coming Tom? Our evac is over there."

"Yeah...I'll be along." His voice was numb.

...

"EDI, where's Tom at? I need to talk to him."

"He's in the bar, Commander."

"Great, just what I needed thanks for the help EDI."

"You're welcome."

...

When Commander Shepard arrived at the bar, he saw Tom in a very sorry state. He was lying on the couch, two empty bottles of alcohol in both hands, he had gotten himself extremely drunk. He was snoring loudly.

Shepard checked his vitals. He'd be fine, he just had to sleep it off. The bigger issue was why? Why did he drink himself under the table like this? Grief was a possibility, especially since him and Legion were probably friends, but he hadn't grieved like this when Mordin died. He just went to sleep earlier then at his normal time.

That was it, he wanted to leave consciousnesses when grieving, that was his way of coping. It worked, sort of anyway. He always tried to keep a straight face, especially in battle, and that was something Shepard could admire, his discipline was similar to a solider following orders, but it seemed a little more personal, but that was expected, he was Commander Shepard, and if anyone could earn the loyalty of his crew, it was himself.

He'd save that question for later, right now he had a meeting with Admiral Hackett.

...

"Shepard good work on Rannoch, I never thought I see an alliance between the Quarians and the Geth in my lifetime, but it's certainly is a welcome surprise."

"It's a shame it took a war for them to do so, sir."

"I agree, but we have no time to think about what we could've done, now on a more important note, we've almost finished the Crucible."

"How long do you think I'll take to complete it?"

"It depends on how much resources the Catalyst needs, because as it stands right now that's the only part we're missing and it doesn't say much more then the name of the part we need."

"I'll see if I can find out what it is, sir."

"Find the answer as soon as you can Shepard, Earth isn't doing well and we won't last long in this war if we try to beat the Reapers conventionally."

"I understand sir, I'll try to find a lead soon."

"I've sent you a message on your terminal that should point you in the right direction, that's all the time I have now, Hackett out."

XXXXXXXXXXXXX

What time was it again? Tom could hardly remember. He felt very wrong, his vision was blurry and all of his movements were sluggish.

"Uhh, Section what did I do in the past three hours?"

 _You were given two bottles of alcohol from James Vega, and then proceeded to the bar where you drank both bottles, one at a time, you had an extreme amount of alcohol in your system, but you should be fine in several hours with proper rest._

"Oh okay, that makes more sense, I think I'm done grieving, I sure hope I don't make this a habit.

 _It was interesting to see an organic attempt to grieve by intoxication, why did you do this? I don't understand the logic behind intoxication, and although Legion was a 'friend' he would not want you to intoxicate yourself to such a degree._

Tom sighed. Bloody AIs.

"It's an organic thing, don't question it, you'd have to be an organic yourself to understand my answer."

 _Understood, I'll be on standby if needed._

There wasn't anything to do, so Tom decided to check his messages, there weren't any. He sighed, time never went fast when he wanted it to, only when he didn't want it to. He had a hell of a hangover. He groaned

"Hey, I see you've awoken, why do you always try to lose consciousnesses when someone dies?" Shepard was standing in the doorway.

"Oh, sorry I didn't see you there." Tom was surprised. "It's just how I cope, I have to drown out my problems that way, I just feel so guilty, survivor's guilt you know?"

"I understand the feeling, you know that your going to have a bad hangover right?"

"I'm already feeling it, I think I'll skip the next mission."

"That's to be expected, get some rest Tom, I need you at 100% when I need you on the next mission, also Chakwas might have something for that hangover."

"Really? Thanks for the tip, I think I'll go see her now."

"You're welcome."

XXXXXXXXXX

Shepard powered on his terminal, and just like Hackett had said, there was an urgent message for him. Shepard took a minute to read it over, he nodded satisfied. If this Dr. Bryson had info that could help him in the war against the reapers then he would take all the help he could get.

"Joker, set a course for the Citadel, I have an important business there."

"Yes Commander, setting a course now."

...

"Hello Shepard, I was told you were coming, we're nearing a breakthrough and you could use your help."

"Hello, Dr. Bryson, what's your assignment?"

"My assignment was to investigate myths, legends and anything of that sort before the Reapers started invading, most of them concerned the Reapers themselves, and now that they've come in force I've been tasked to investigate their origins, anything which will tells us why they're crusading across the Galaxy, and of course to possibly find a weakness after we know their origins."

"I could've used your help three years ago, so what info do you have for me that could help?"

"We're nearing a breakthrough, my assistant Hadley is actually gathering it on a datapad as we speak." Bryson took a breath, and that's when Hadley decided to walk in.

"Do you have the data?"

"Yes sir, it's all here, make sure this gets into good hands." His voice was somewhat monotone, and little unnatural.

"Thank you, continue with the work I talked about beforehand."

"Yes sir."

"He sounded a little...off, putting it mildly." Shepard was concerned.

"He's been acting like that for a while now, but I'm not sure what the cause is, but it doesn't seem to be anything worth looking out for, he's proved to be very helpful over the past three days, so I've ignored it to a point."

"To a point?"

"I tried questioning him at one point, but he kept deflecting the question, I didn't want to probe too hard as I would risk him quitting the job so I stopped, I just hope whatever's happening to him isn't detrimental to his health, but I'm rambling, let's get back on the topic."

"So these coordinates, what are they for?" Shepard was reading the datapad

"Those coordinates contain the estimated location of where the Leviathan is located, I do not know for certain, but most of my evidence points to them hiding on the planet 2181 Desponia."

"And I'm assuming that's where I come in." Shepard had been asked for help so often that now he knew when people needed him.

"Precisely, I don't know if these Leviathans or whatever are going to be friendly or not, and my people are non-combatants, you're well equipped to deal with this, and if the dossiers are correct you already have a former archaeologist on your team."

"That would be Liara, I'll investigate, I'll tell you if I find anything Dr. Bryson."

"Thank you Commander, I'll be here in this lab when you get back, so come visit me when you get back when you have the chance."

"I will, stay safe, the Reapers may try to silence you somehow."

...

"Joker, I'm uploading some coordinates, I need you to head there, we've got an old myth to track down."

"Yes Commander, it's going to take around 12 hours to get there, but we will, you know, eventually."

"Yeah, yeah, just get there."

XXXXXXXXXXXXXXX

"You know, I wasn't expecting Shepard to do that, nor was I expecting Legion to die, I'd never admit this to anyone other then you Tom, but I think I'm going to miss Legion as well." Tali was perturbed.

"The guilt is getting to me, but this war is almost over, at least I hope so, with the help of your people and the Geth, we have a much better chance then we did before of winning this war, mind if you can refresh my memory of how your people and the Geth are interacting?."

"The Geth are doing in weeks what have taken us years, infrastructure is being built as we speak, day and night, if there's one thing nice I can say about the Geth it's that once they're set on a goal, they don't stop."

Tom activated his countermeasure, ensuring that EDI wouldn't know what was going on in this room. "I tried my best, you know."

"What?"

"I tried looking at so many different solutions to save Legion, but I couldn't, it's eating away at me now, even after I drank myself under the table."

"Just know that I don't blame you, knowing things like that will weigh you down, keelah, being the daughter of an admiral puts a lot of pressure, I know how you feel, do your best to learn from your failures, it's what I did on my pilgrimage before Shepard came to me."

"Thanks, that helps more then you think, I just hope that at this point I've done everything I can to help Shepard, he deserves it."

XXXXXXXXXXXXXXXXXX

"Hackett, we're on route to investigate the Leviathan, I'm hoping we'll be able to find something that'll help us win this war." Shepard said.

"At this point, hope is all I can give you as well, we both know that it'd be impossible to win against the Reapers conventionally, the Crucible is our only hope, and maybe the Leviathan, what ever it is, may lend us a hand."

"With all due respect, sir why me? I know that I helped stop Saren and the Collectors but there's more N7's out there, some of which are better then me at fighting, why me?" This was one of those rare moments where Shepard was forlorn.

"Shepard, I know there's better people out there then you, but the reason it's you who's dealing with all of this is because of this one simple fact. You can pay Soldiers to shoot things, defend things, and in some cases negotiate, but you can never pay a Solider to believe they're going to win the war. That's why you're in charge, because you believe, and I need people like that."

"That's humbling, sir."

"It's the least I can do Shepard, keep up the good work, myself and the rest of the Galaxy is counting on you to take down the Reapers, Hackett out."

That was very humbling, a lot more then what Shepard had said. He didn't care about a lot of people in this Galaxy, it wasn't a good place, people were always looking out for themselves, that was how it was when he was hunting down Saren after all. He rubbed his eyes. He was tired, he'd better go to sleep before Chakwas eventually force fed him some sleeping pills like she did on the original Normandy.

...

It was that bloody kid, again. He kept being set on fire just before he could be saved, and this time he'd actually seen himself burn with the child. Was he indoctrinated? At this point he probably was, but they way the Reapers were doing it was weird. Sure, he couldn't save that kid, and that made him feel guilty, but you could only guilt someone so many times with the same thing before they became numb to the whole thing, and that was starting to happen now.

"Shepard, we're 30 minutes out from that planet that you wanted me to fly to, you better get your guns of what ever." Joker's voice rang out through the intercom.

"I'll be there in a minute Joker." Shepard said. The man sighed wearily, this war was tiring him, he needed to end it soon.

* * *

Reviews:

 **Squadpunk 2.0:** Here it is.

 **redcollecter:** Well, was that enough?


	18. Chapter 18: Bleed

"So what are we expecting down there?" James was raring to go.

"We're trying to find an ancient species, they're called the Leviathan, but it's hard to find where ever they are on a place like this." There was a raging storm outside, and by the looks of it, not much landmass to land on.

"Is this why I'm here?" Liara questioned.

Shepard turned to her. "Yes, just because I believed that your previous experience as an archaeologist might be handy."

"So what do we know about these Leviathan?" James asked.

"Apparently they're strong enough to disable a Reaper easily, which is something you can think would be useful if we had it on our side."

"Do we know anything about their origins, or their motives?" Liara asked.

"No, I didn't get much information about them, in fact I'm not certain that they're even on this planet, but we have to try and find them regardless of that."

"Commander I'm picking up a Reaper signature in orbit, it's coming down to the planet's surface now."

"Cloak our heat emissions, even if they can see us we're not going down without a fight, I don't plan on dying today."

"It's far enough away to prove a minimal threat, but we can't get too close without getting shot down, I believe it's seen us, but it appears not interested in us at the moment. "

"Well, I guess this is the right place then if a Reaper's interested enough to investigate, I'm going to assume it's also after the Leviathan."

"Commander! I'm picking up some sort of pulse originating from deep below the water, it's trajectory is right in the path of the Reaper, orders?"

"Let's just watch this happen, don't stay close, fly a bit further away so we don't have to worry about getting hit by it."

Everyone watched in the cockpit as the pulse instantly disabled the Reaper in a single shot, the Reaper fell into the water, sinking down to the murky depths where it would lay forever, the pulse was barely visible when it hit, but when it did the red sparks of energy sparked across the Reaper's hull before it fell into the water.

"Holy hell! It disabled that thing in a single shot! It didn't even take a year for it's shields to break, it just died!" James was surprised.

"I'm more concerned about another thing, how are we supposed to get down there? The Leviathan itself is probably a thousand or something feet below the surface, how are we going to get down there?" Shepard evidently was more concerned about the task at hand.

"Commander, this shuttle was built to withstand extreme heat, cold, and believe it or not, it can withstand the pressure of being underwater for prolonged periods at once, in theory we should be able to go deep enough to see the Leviathan, at least if the manual is to be believed."

"Well, there's only one way to find out, Cortez, take us in." When the shuttle actually survived under water Shepard let out a breath he didn't know he was holding.

"What are we supposed to do when we find them?" James was pacing slightly, he had energy which wouldn't go away, he was expecting a fight, not a shuttle ride.

"Relax, you're going to wear out the floor the way you're pacing, why is that?"

"I'm just full of nervous energy, Commander. A death at the bottom of some random planet's ocean is not how I wanna die."

"Dying wasn't on the agenda, I'll make sure we get out of this, it'll be fine." Shepard reassured. He looked out the window, they were getting very deep under water, he could see some alien flora and fish, there was barely any light down here, the lights on the shuttle were the only thing that had light down here, it was slightly unnerving.

"Commander, we can't go much deeper, only a little bit longer and the pressure will start to break this thing."

"Take us as far you can, but not any lower, I was tasked to find the Leviathan, but I'm not going to kill myself trying."

"Yes Commander."

Shepard turned around, only for everything to be grey. He spun back around, everything was gone, there was nothing, where was he? He didn't remember dying or any of that, where the hell was he? He suddenly felt the sensation of being in dark, cold water, it was extremely unnerving.

"Hello? Is anyone here?" He called out.

"You are an anomaly, but that's enough to be different, to defy the odds."

"Who's there?!"

"We are the Leviathan." Shepard turned around to see Bryson's lab assistant.

"Hadley?"

"Simply someone to visualize in your mind. We are the Leviathan, and you are an anomaly."

"What do you mean?"

"You defied the odds by destroying the one known as Sovereign, you've destroyed other Reapers, this has never happened before."

"What do you mean?"

"We have been here since the beginning, before the cycle started, before the Reapers began their harvest."

"I've heard that one before, what's this harvest you speak of?"

"The harvest is a cycle which repeats itself every 50,000 years, at the end of every cycle the Reapers come and scour the galaxy, taking all organic life and storing it in the shell of a Reaper, one Reaper which you would consider Sovereign class is the equivalent of a dominant and fruitful species. In scope a civilization like this would be similar to the Asari."

"Why do they do this?!"

"It's a system of our own make, turned against us, when the Reapers didn't exist we were the Apex race, but we realized a pattern over the lesser species, synthetics would always rebel, so we created an AI to stop that from happening, in the end we were foolish enough to treat it like a tool like everything else, in the end the one you know as Harbinger was the first Reaper, created from my brethren and in the image of our species."

"Seems awfully a lot like the other races creating their own synthetics who then turned against them, that's awfully ironic for an 'apex' race."

"It was our own arrogance that was our downfall, we assumed we could easily destroy it if it turned agaisnt us, in the end we didn't have the foresight to think about the consequences of our own actions, but regret is a waste of time."

"Can you help me? We could use your help in the fight agasint them, we could never win this fight conventionally."

"We cannot provide any sort of tactical support in this war, the Reapers would hunt us to extinction, but we have seen your plans for the Crucible, it has been completed before, but it has never fired before, indoctrinated agents made sure of that."

"Then can you tell me what the catalyst is? That would at least help us build it."

"The catalyst is the Citadel itself, it draws energy from the Reaper's own creation and turns it against them, but the intelligence would ensure that any attempt of destroying the Reapers would ensure massive collateral damage, we've uploaded a virus onto your primitive Omni-tool which will disabled the intelligence long enough for you to make a decision without it interfering."

"Thank you, is there anything else I should know?"

"No, this exchange is over, finish the crucible and destroy the Reapers and end the harvest."

"My only question is how the hell can I trust you?!"

"The Reapers slaughtered us as well as everyone else when they cycle began, we want revenge, just like all of you, finished the Crucible and destroy them, this cycle has the best hope of destroying the Reapers."

Shepard couldn't remember when he woke up, but they weren't on the shuttle anymore. He had a bad headache and his nose was bleeding.

"Commander, are you alright? You were unconscious for a little over 3 hours and James made an executive decisions to bring you back to the Normandy, are you alright?"

"Yeah, hell of a headache though, I'm going to go debrief them, they deserve to know what happened."

"You also had some of the most unusual brain activity I've seen, your brain waves were changed it such a strange way, mind if you can tell me what happened?" There was no point in lying.

"The Leviathan...they spoke to me, they had mind control properties similar to the Reapers, but a bit more...refined, I still have a bad headache though, so it obviously isn't perfect."

"You'd better include this in your report, the Alliance will want to hear about it, you're free to go at the moment, the only issue I see is a headache and I didn't see anything detrimental to your brain or health while you were unconscious."

"Thanks Doc, I'll be going now."

...

In hindsight the catalyst being the Citadel was actually a genius move. How could you destroy a force so massive with a single shot from a weapon? Simple, turn the their own relay system against them. That was actually a genius plan.

"EDI, get me Admiral Hackett on Vid Comm." He said purposely as he speed walked down the CIC.

"I'll try my best to raise him."

...

"Shepard? What's going on?"

"I know what the catalyst is, sir."

"How did you find this information?"

"My report has the details, all you need to know is that the catalyst is the Citadel. Think about this, the only way we could defeat the Reapers is by using their own relay system against them, and the Citadel is the Relay control, in hindsight it's a genius engineering move from what I can tell."

"This information can definitely win us the war, thank you Shepard, you're saving a lot of lives."

"Just doing my duty."

"Also, there's one thing I've been meaning to talk to you about."

"Sir?"

"You know those advertisements about Sanctuary? The one on Horizon?"

"I've only heard it through eves dropping on some scared colonists that wanted to move there."

"Apparently it's a Cerberus facility run by some Lawson's father, that name doesn't mean much to me, does it to you? We lost contact with the mole shortly after she mentioned looking for her sister, does any of this hold any weight?"

Shepard's expression hardened. "This is Cerberus alright, they're probably up to no good, I'll stop them while you coordinate with the engineer's working on the Crucible."

"Get to it Commander, Hackett out." He ended the call.

"Joker, set a course for Horizon, we have a Lawson to save."

"The Ice Queen? Setting a course now Commander, I figured she probably be trying to do some damage to Cerberus as this point."

"You bet, I just hope we're not too late."

...

It was a slaughter when Shepard and his team consisting of Garrus, Kaiden and Tali stepped out of the shuttle which had landed close to the landing pad where a couple of Cerberus troops were gunning down fleeing citizens.

"Garrus start sniping, NOW! Tali stay on me, and Kaiden try to distract them while me and Tali flank them, this is going to be messy." Shepard said as he drew his Claymore.

It was a quick and bloody fight, Cerberus troops fought as hard as they could to buy time for their scientists to pack up, they were dug in and had superior position, but with Shepard and Tali flanking, and a sniper to keep the troops in cover they dealt with it quickly, they were getting hit on all fronts and didn't last long.

Shepard wiped a bead of sweat from his forehead after shooting the last solider. "That was tough, but stay frosty, we've got more Cerberus goons to clean up."

Any civilians that were fleeing were getting gunned down by any Cerberus troopers in the vicinity, they were making sure no one left, alive or dead, most bodies were burned as well as shot. There was a rough firefight when Shepard and co. got past reception, it seemed that they were specifically tasked to stop Shepard as they were packing heavy weapons and sniper rifles for brutal long range fights that were riddled with explosions and AP rounds.

They were pinned down for a while until they got help from an unexpected source, one of the sniper's suddenly stumbled back before screaming, and then promptly got lifted in the air before being smashed, triggering a biotic explosion from the combination of a warp and a slam. This decimated the two heavies and the other sniper that had the high ground.

Shepard holstered his gun when he saw who it was. "Miranda, you're the mole?"

"Let's just say I had contacts that let me get inside undetected, I assume you got my message?"

"Hackett didn't know what to make of it, but you got it across pretty clear, what's the situation?"

"Cerberus has killed 90% of the civilians, the rest are either hiding or captured, my father himself is holding Oriana hostage on the top floor, we've got to get up their before he kills her."

"That's just great, do you know how to get up there?

"Of course, I'll lead the way."

...

Resistance was fierce, but not very strong, the soldiers fought hard, but there weren't many of them, it seemed like they were running out of manpower and reinforcements, it seemed like the Illusive man had decided to pull the plug on this operation, and that everyone here was going to be discarded as useless. At the elevator they tried to use an improvised bomb that Garrus and Tali both quickly disarmed, they were definitely desperate.

There was some nervous shouting when they reached the top of the elevator.

"What are you doing? Don't leave me here! I'm useful!"

"Your projects didn't yield and interesting results, Lawson, my research made much faster progress and was much more cost efficiant, your operation is over, you better hope Shepard has enough mercy to spare you, but I doubt that, goodbye Henry."

"You asshole! I'll-" The door opened, Shepard and co. entered, weapons drawn.

"As expected, Shepard I'm walking out of here, Oriana is coming with me." He was clearly trying to mask his nervousness as he held Oriana at gunpoint.

Shepard chuckled. "This is what you get, a deal with the devil always ends with him abandoning you, did you really think I'm going to let you out of here? You're a dead man Henry, and now that fact is going to ring true."

Shepard aimed his shot and fired.

* * *

A/N: This chapter seems a little rushed, at least to me, but you can be the judge of that, I've tried to not leave any plot holes because I want my story to be somewhat believable.

Reviews:

 **redcollecter:** I'll be getting to that.

 **general-joseph-dickson:** Glad it passed as a good chapter to you.

 **Guest:** If you're talking about Dr. Bryson then the answer is yes, I hated how he died right as you talked to him as it would've been cool to save him in the DLC as he could've saved us like 3 missions worth of searching for the Leviathan, plus his character is really cool.


	19. Chapter 19: Bury it

It was a perfect, clean head shot, right through the skull. Henry Lawson died right there. Oriana, being a civilian wasn't actually very shocked after seeing a dead body, but after all the bloodshed she had witnessed, this was nothing. And she had her sister for comfort.

"Oriana, are you alright?" Miranda's voice was filled with concern.

"Ye-s I'm fine." She stuttered.

"Henry Lawson is dead, I guess your nightmare is over now, Miranda."

"Yes, thank you Shepard, I wouldn't have gotten past all of them without your help, now I can finally rest easy knowing that bastard is dead."

"Man, still need my help huh? Soon you're going to need me around to take out one soldier." Shepard abruptly kissed Miranda, which she returned passionately. The moment was ruined however when Oriana screamed like a little girl.

"Oh my GOSH! I KNEW you were with Shepard I KNEW IT! You two are sooo cute together, I totally ship you guys!"

XXXXXXXXXXXXXX

The Illusive man was not pleased. His top agent had been killed somehow, most of his operations had been destroyed by Shepard, and he was losing resources faster then he'd ever had before, the fact that Earth, the place where 60% of his funding came from, was under attack was even more worrisome, but that could wait, he would retake Earth after the Reapers were under his control, and humanity was the dominate species in the galaxy.

Right now he had to ensure that he had the means to control the Reapers, he needed to begin the procedure, his augmentations were going to be needed for this next step. He touched the intercom.

"Get me the Docters, the project is beginning now."

XXXXXXXXXXXXXXXX

...

Your orders are to take the station, destroy all of Cerberus' resources and prevent them from disrupting any more war efforts, are we clear?" Adam asked, looking over the mishmash of species that were the best of the best, determined to take the station. Everyone saluted, this was going just as planned. "N7's, get coordinating with our Counter terrorism Units, Blackwatch, work together with the Quarians, you guys will be forcing an exit and escorting several teams into the station. And all the Krogan, your going in first, we've got a long day ahead of us, let's show these Cerberus bastards that disruption of our war effort will not be tolerated!"

The Illusive man had certainly fortified the station well, there weren't many locations where it was a viable tactic to enter, had this been an all human Op, Alyona thought this would've failed, but with the Krogan their entrance strategy was much more flexible, as Krogan were fantastic shock troopers, able to take a lot of punishment and dish out about as much, although they were very vulnerable to snipers.

That's why he decided on leading his small team of two Krogan, a Turian blackwatch sniper, and a couple of his friends from the Spetnaz into a small airlock where hallways were very close quarters. He sighed. Most CTUs had been disbanded after the Reapers hit Earth, mostly due to losing most, if not all of their members. The Reapers knew almost exactly where to hit, it's almost like they'd been to Earth before, it was actually terrifying how fast they destroyed the resistance in most cities. Now was not the time to be thinking about that though, he readied his shotgun, this was likely going to be a long mission. He wished had had an N7 to lead them, as they were a force of nature, oh well, he'd make do.

XXXXXXXXXXXXXXXX

He had the base on red alert, several infiltration teams had somehow bypassed his security and made onto the base, he made sure the labs were secure before he finished the second half of his procedure. It went just as planned, now he was the perfect human being, his new upgrades allowed him to control the motor functions of other people remotely, he had no doubt in his mind about this being the right thing to do, now he had to stop Shepard, and if he had to, he would do it in person.

"Get the ship ready, and get my top agents to it, we're going on one last mission to end the Reaper war." The Illusive man looked around at all of his scientists, most of them working frantically to secure data. He walked out the door, and sealed it on his clearance, none of them were getting out that, they were expendable. That was the only exit. He walked towards the docking bay, he had a lot of work to do. Humanity would be the dominant species in the galaxy when he was done.

XXXXXXXXXXXXXXXXX

"Good work done there on Horizon Shepard, Cerberus is losing resources fast, and the attack on their main base of operations is happening now." Hackett had a rare smile on his face.

"How's the attack going?"

"Well, we've successfully infiltrated their base, we're moving to destroy it now, the only hiccup is the fact that one ship managed to get out before our team secured of the last docking bays, and it was too fast for any of our ships in the vicinity to get it before it jumped to the Relay in the system, it had incredibly advanced stealth systems, similar to the Normandy's if my Ensign is to be believed."

"Have you gotten the Crucible to the Citadel yet?"

"It's there right now, we're just working it out with the council right now actually, we'll probably have worked something out soon however, everyone is tense and I don't think they're going to want to refuse."

"Well it'd be suicidal to refuse, I think I'll make a stop there just to see how it's going."

"Keep up the good work Shepard, Hackett out." The call shut off.

"Joker, get us to the Citadel, I need to meet with Bryson and it'll be a plus to see the Crucible go off."

"Yes Commander."

XXXXXXXXXXXXXX

"I guess I did it, right? I altered everything in just the right way to ensure the Crucible is not activated under the control of the intelligence, right?"

"Although crude, this did lead to the correct outcome, the virus will freeze the intelligence for long enough for a suitable choice to be made, we've made a backup on your Omni-tool in case of the death of Shepard." The unnamed Leviathan said.

"It's still crushing me though, seeing Earth like that...it's extremely disheartening, I wished I could've done something, anything, to make Humanity more prepared, I can just see them all pinning it all on me, in all honesty I hate it, I could've done something, and I didn't, the ruthless calculus of war may work, but it sure is a hell of a guilt trip, and I don't enjoying sacrificing people for the greater good, the ends almost never justifies the means, I've learned this through the Illusive man."

"Regret is a waste of time, as is emotion, we'd thrown those thoughts aside long ago."

"How can you say that? You're own species was hunted to extinction and you don't even grieve, where the hell did your motivation go? You sound like a machine, but I guess you have a reason because your 'beyond my comprehension' or whatever bullshit you can spew out. Remember that I'm winning this war not for you, but for the people that deserve it, like Shepard, I'm not your servant or bloody puppet, I'm someone who's about to end the Reaper war, good bye, think about what I sai-" The connection was cut abruptly.

What the hell? That was definitely not intentional, what ever, it was time to space this stupid ring and end all this crap about being a servant to the Leviathan, if there was anyone that deserved him being a servant to, it was Shepard, not some Cthulhu squid thing that thought of him as a tool more then anything else.

He spaced the ring without regret. These last few conversations with the Leviathan were starting to make him think that they were going to discard him after this war was over, he was a threat to them, wasn't he? He wasn't going to be a puppet any longer, at least Shepard earned the respect when he commanded people. The last few conversations were uninteresting at best, and completely a waste of his time at worst, most of the times it was just to talk about how they'd be glad that the Reapers would be destroyed and how effective he was.

XXXXXXXXXXXXXXX

The war was almost over, at least that's what Hackett thought, he was definitely not expecting a Cerberus ship to suddenly materilize right next to the Crucible's docking point with the Citadel, and unfortely he couldn't take it down. It's not that the Admiral didn't want to shoot down the ships, it's that he'd risk massive collateral damage if he did, which was probably an intentional move, they had probably planned this as part of their attack

"Get me the council, now." Hackett said as he raced across the deck to get to his QED. He'd have to get them to divert C-Sec resources to the area of he didn't already, and he'd airdrop some marines to ensure they could stop Cerberus, Shepard also had to hear of this, he was the Alliance's most effective asset at dealing with Cerberus, and he'd probably be able to activate the Crucible as well.

XXXXXXXXXXXXXX

"Shepard, Admiral Hackett wishes to see you on Vid comm."

"I'll be right there, I'll talk later Garrus."

"I'll be here if you need me Commander." He said faithfully before turning back to continue calibrating the Normandy's main gun.

..

"What's the situation, sir?"

"That one ship that Cerberus got of their station? It managed to slip past shield fleet, it just forcibly docked the Citadel, how close are to the Citadel?"

"I asked Joker on the way up, he said around 30 minutes, we can provide support on the ground if you need."

"I do Shepard, I'll try and call up some of our allies that you've gathered to help if I can, I need you to secure the Crucible and activate it before Cerberus can disable it, is that clear?"

"Yes sir."

"Good, Hackett out."

How the hell did this happen? Shield fleet should've been able to take down one ship, what went wrong? Shepard found himself asking these questions as he walked out of the CIC and into the elevator. He'd stop them, then he'd end this war and live off the royalties of the vids, he could almost see it now, but like his mother had once said.

 _Don't count your chickens before they hatch._

He stop this war first, then he could relax.

...

"Liara, Garrus, Tali, Tom, James, EDI and Kaiden, suit up, we're about to stop Cerberus from disabling the Crucible and finish this war, get down to the shuttle bay and suit up."

...

Fighting was brutal on the ground, now Shepard hadn't regretted taking his entire team with him, he's needed the extra firepower, Cerberus was mowing down anyone who got in their way, on the Presidium where they landed were several squads of troops, and two giant atlas mechs, it seemed like they were a blockade force as they weren't progressing at all and were shooting anything that breathed.

"Garrus, Tom get on top of that balcony to our right, I want to make sure we've got some snipers up there to counter any they may have, everyone else on me!" Shepard shouted before shooting a Guardian through his shield. Shepard and co. managed to provide exellent cover fire as Garrus and Tom made a push for the stairs that led to the balcony that ran the length of the battlefield.

"Set up shop Garrus, I've got your back." Tom said as he pulled out his pulled out his Mattock which he was going to use as a DMR with the scope he had added on. There were two Nemesis snipers up here, both of them were more concerned about Shepard and his squad, and they weren't looking when Garrus and Tom had made a push to the balcony.

"When I say now, overload one of their shields so I can take the shot."

"I gotcha."

"3...2...1...NOW!" She lost her shields, after that she lost her life.

Unfortunately the second sniper noticed this and started shooting at them, Garrus managed to get an overload to break her shields but was forced to take cover after that. Tom started blind firing and when he eventually stopped he noticed that the other sniper wasn't even shooting anymore, he looked up and a little bit of her dead body was showing, slumped over the railing he had scored a lucky headshot.

"Both snipers down, let's start sniping them now."

Shepard and his squad had taken down most of the ground troops, now it was just the two mechs that were giving them trouble since their armor was taking quite a lot of punishment. With Garrus and Tom though that advantage was mitigated as a couple rounds from a Widow broke the glass, the pilot inside the first Atlas immediately died after that, and then the second Atlas fell easily as well due to the same fatal flaw.

"Nice work up there boys, now get down here with us, we're near the Crucible."

The only reason they hadn't landed ON the Crucible is because Cerberus had forcibly shut every single one, there was only that one elevator that Hackett had told Shepard about on the Citadel that they could go from, and it was heavily defended. Fortunately there were no Atlas mechs due to the corridor being too tight to fit one, but there was no cover and a ton of troopers with their guns pointed at Shepard and co.

The firefight was purely who shot first due to there being no cover on both sides and the elevator being occupied, meaning that no Cerberus goons could take cover in it, Shepard's squad won purely due to having more powers, either biotic or tech, and that made it much easier to kill the Soldiers when they were either on fire, frozen or screaming as they were ripped molecule for molecule, or just pure meat from a grenade.

"Any injuries?" Shepard said after seeing the hallway clear.

James spoke up. "I took one to the gut but it didn't get through my skin and Kaiden took one in the leg."

"Take my Medigel, you're going to need it, now we're going to need to have some people defend this point so they can't follow us up when we use the elevator, Garrus, Tali and Tom come with me, everyone else, hold this elevator, make sure no one else gets through, I'll radio if we need help or when we're coming down, is that clear?"

There was a respectful silence as the people being left behind nodded.

"Good, good luck down here, let's end this war."

* * *

A/N: No chapter next week since I have a life and am going on vacation. Also, don't ask about the ending. I decided to do the ShepXLawson pairing because I find it's seldom done, and needs a bit more attention since it's neat to see Lawson under all that cold ice.

Reviews:

 **redcollecter:** I think this chapter just answered that question.

 **stormdragon981:** More guns are better, right? The more the merrier. And plus Tom didn't actually need to make too many significant changes to alter the outcome to be better then the Crucible being activated on Earth.

 **Guest:** Yeah, Bryson is going to stay alive, but I'm not at a liberty to say where he is, he is healthy and not dying though. There was so much wasted potential in character development there, I hate games where they introduce a somewhat important character only to kill them off immediately, it wastes so much there. Thanks for being fair and telling me you're the same guy by the way.

 **general-joseph-dickson:** Learned what exactly?


	20. Chapter 20: End it all

It was tense on the way up, no one said a word as the elevator reached the highest possible floor which opened out to large hallway, where everyone had to immediately duck back inside to the sides of the elevator due to there being a ton of snipers and Centurions. Although that problem was solved with a couple inferno grenades Shepard had. He had that explosive grin on his face as he pulled the pin and threw them inside.

The resulting explosions was quite heated to say the least, a quarter of the people in there were set on fire, none of them lived after that as they were quickly picked off. The snipers were a bit more of an issue, due to having their guns constantly pointed at the door, so if you poked your head out for more then a second your shields would be gone, then your head would be too if you were too slow.

Tom and Tali took care of this with the use of their respective powers, Tali used her combat drone to force them out of cover, and Tom would just cloak, get a head shot off with his Widow and repeat, some Centurions tried to get close, but a defense drone prevent them from getting any closer. In the end the only ones left were the Centurions, and a barrage of powers took them down, Concussive shot, disrupt, shield drain, Cryo blast, Incinerate and a handful of grenades.

"Nice job, it looks like we broke through their welcoming party." Shepard commended.

"Shepard, I think you might want to take a look at this." Tom said, he was a little bit of ahead of the group, staring at a dead body.

"Spirits" Garrus muttered as everyone saw the pile of dead C-sec and Alliance troops, in clustered pile together on the side of the hallway.

"They ambushed these guys, they probably never stood chance." Shepard said bitterly before taking the dog tags off each of the Alliance Soldiers.

"There's nothing we can do for them now, let's keep moving, the only way to honor their sacrifice is to win this war."

 _Meanwhile_

Anderson activated the QED, hoping Hackett would respond. He did, this was good.

"Anderson, what is it? This was marked as an emergency call, what's wrong?"

"It's not about us sir, we're still getting decimated out here, it's the Reapers, Harbinger just broke off his attack and is making is way to the Mass Relay, I think he's going after the Crucible."

"Did he just break off his attack immediately?"

"He pulled a turn that could shear your ship in half and started gunning it towards a Mass Relay, that was a couple minutes ago, although it's a welcome relief that he isn't attacking us anymore, it worries me that he left with such haste since most things don't bother the Reapers."

"Thanks for the info Anderson, this is a good heads up."

XXXXXXXXXX

They walked for a bit through the Hallway, there was a lot of stairs and eventually, a lot of Cerberus, and there was a lot of dead scientists too, which disgusted Shepard. It was an uphill battle this time, the Cerberus troops had the high ground, and this would normally be an issue, but it wasn't due to their force being made up of Phantoms and Guardians, this was a blockade force, trying to make sure no one got through. The phantoms were easily taken care of after seemingly receiving an order that made all of them charge down the hill at Shepard's squad, which was completely suicidal since they're barriers may have been good, but with Shepard's orders to focus on one at a time they seemed like cardboard from combined fire.

The Guardians were a bit trickier since they actually held their positon, but with a couple more grenades, Tom flanking them, and an Attack drone, they were easily taken care of after proper plans were pulled off. This took significantly longer, but in the end Shepard did win, with minimal injuries too, he was the only that got injured by taking a shot to the gut.

"I'm fine" he said, brushing them off, he did get some Medigel on so it wasn't going to be a big deal.

It seemed Cerberus was running out of troops too since they only ran into groups of three at a time, and most of them had an attempted suicide bomber, but they were picked off by either Tom or Garrus before they could be a threat so they didn't have any problems, when they made it to the stairway that led to the controls they were a little low on thermal clips, but they were almost done, right? They could go home after this.

At the top there was one lone figure in front of the control panel that activated the Crucible, one man. The room was littered with corpses of scientists.

It was the Illusive man.

"I underestimated you, Shepard, I didn't think all of you would make it up here, but it's over now I have control." He turned around, revealing an abomination of circuitry on the left side of his face. He belonged to the Reapers now. Everyone raised their weapons, but then they all felt suddenly not in control of their own body, like it had been stolen from them.

"Why are you doing this? The war can be ended with the Crucible! Are so blind to the indoctrination that you don't even realize your stopping the people that are going to save this cycle?" Shepard said angrily.

"I can't have you do that, not after everything I've worked for, I know the Crucible will let me control the Reapers, and I intend to do that to advance Humanity to the top of the Galaxy."

"Why aren't you doing it then?! You've been sitting here this entire time and haven't even pushed the button? You're pathetic." Shepard chided.

He snapped at Shepard. "Don't lecture me on why I haven't! I've been...thinking about how to work this out, you're complicating the matter." He said.

"It's no use, they own you now, as soon as you had that Reaper tech implanted in your face they've owned your every thought, you just don't know it." Tom said.

"No one's telling me what to do! I'm in control here!" He shouted, but he was getting more concerned with every single word that came at him.

"Then activate the Crucible, you bosh'tet! We're waiting!" Tali said.

He looked like he was about to to, turning to face the console, but then he turned back around. "I'm sorry, I just can't do that."

"It's just like Tom said, they control you now, even though you're so blind you don't even realize it, you can help us win, just let go of us for a second." Shepard pleaded, letting The Illusive man have a chance at redemption.

"I-I I'm sorry Shepard, I tried to fight it but after a while it controlled me too, I can't do this, they demand that I kill you, but I won't. I was a fool to think I could control them, and now I need to stop you from getting to the control panel, but I won't." He took the pistol and almost pulled the trigger on his own head when a voice Shepard knew very well boomed throughout the room.

 **"That won't be necessary, assuming direct control."**

"What? No!" The Illusive man screamed as his entire body and mind was overpowered by the Reaper, Jack Harper now no longer existed, Harbinger had destroyed the little bit of him that was still there after the indoctrination.

"Harbinger." Shepard's voice held enough venom in it to kill a man. "Light him up!" He ordered before pulling out his Revenant and going to town on the Reaper. His barrier however was incredibly strong and took all the damage from the two snipers, shotgun user and one assault rifle user with barely any issue, then he struck back with a black ball of pure energy.

It slammed into Shepard, which disabled his shields and set him on fire a little bit, but Shepard just grit his teeth and kept firing. That's when Tom decided to act, since all of Harbinger's attention was focused on Shepard he snuck up behind the Reaper and used his Omni-choke, which effective stopped the entire fight for ten seconds.

It almost seemed too easy until his Omni-tool exploded from the unstable energy it absorbed, his shields took the brute of the explosion, but it had enough concussive force to slam him into a wall at the far side of the room, he felt at least one rib broken as well, which was not good.

"Error 351 Overload detected, rebooting memory, standby." His Omni-tool said as it tried to fix itself from the explosion that somehow didn't incinerate the whole dang thing, he could barely move anyway, his vision was blurred and it hurt to move all over.

This was actually a losing fight for Shepard, Harbinger's barrier was way stronger then it was before, and his energy attacks were hard to avoid and did massive damage if the Reaper landed a successful attack, his barriers almost flat out ignored bullet damage entirely, but they were wearing it down, slowly.

The issue was that there was no cover in the room so your shields wouldn't recharge unless he started attacking someone else for a while, and Tali's drone was a pretty decent distraction. It didn't last however, because soon Harbinger walked right up to Tali and swatted her aside like a fly that had actually started to be annoying, she was slammed against the wall, probably unconscious. Even though Garrus and Shepard were combining fire to take this monstrosity down it wasn't enough, his shields were down to 10% but that was going down slower as two people were already out of action, Shepard still didn't know if Tom was even alive at this point.

8%, 7%, 6%, and that's when Garrus got hit with a ball of black energy while his shield was recharging, which tossed him across the room like a rag doll. Shepard quickly ran over and administered the only two stocks of Medi-gel to Garrus and Tali, hoping that it would keep them alive before he continued shooting Harbinger. He used up his remaining supply of Medi-gel on Tali, there was none left for Tom.

5%, 4%, 3%, he dodged a black energy bolt meant for him before he continued shooting. 2% 1% 0%...and that's when everything went to hell. Right after his barrier went down Harbinger walked straight up to Shepard, punched the Commander with enough force to make him see stars and held him up by his neck.

"Reboot complete." Tom's Omni-tool blinked back into life and then Section quickly administered the remaining amount of synthetic adrenaline that he had into Tom's system. He woke up right there.

"Gah, thank the lord Section, we all would've died here would it not be for you."

"I'm administering the remaining Medi-gel."

"Hold that, I might need it for someone else right now." Tom said as he cloaked and got up.

 **"I said I would tear you apart Shepard, and I will."**

"For all your apparent wisdom and power, you should have never forgotten I had friends." Shepard sputtered as Harbinger's back was lit up by a Claymore Heavy Shotgun that Tali had been using before she was knocked out, Tom had taken it. Tom reloaded, then shot again, and then he did it again, Harbinger was barely standing at this point, so he dropped Shepard and spun around, only to receive a shotgun blast to the face for his effort.

After all of this, Harbinger finally knew what it was like to be torn apart as his body was nothing but a mangled corpse after the third shotgun blast to the face. Tom turned around, looking at the carnage that had happened in the room, and he noticed Shepard, on the floor with several wounds, he walked over.

"I got you Shepard, now let's end this war." Tom said as he helped Shepard up.

"Thanks Tom, you saved my life here, now let's get this thing ready and destroy the Reapers once and for all." He limped over to the console and uploaded the code, it was all gibberish before, but now it actually readable words on it. It had one option on it.

Destroy

"Looks like it's game over for the Reapers." Tom said as he looked over Shepard's shoulder. As soon as the Commander clicked on it there was more information given.

 _Destroy the central intelligence of the Reapers and render each Reaper non-functional, there will be no collateral damage and the only things destroyed will be the Reapers and any of those using Reaper tech, this will effectively end the Galactic extinction cycle that happens every 50,000 years. All indoctrination will be destroyed and all symptoms_ _will be removed. This leaves all Reaper databases intact but the Reapers themselves will be permanently deactivated._

"About time this is all ending, I'm doing it." Shepard had said as he pressed the button.

"Shepard to shield fleet, the Reapers are about to go offline, this attack will only destroy the Reapers and will render them permanently deactivated, there will be no collateral damage. Hold out against Harbinger a little longer, the Crucible is about to finish powering up."

"Thank you Shepard, we all owe you our lives, we'll hold out until it goes off." Hackett said.

It was not long before the Crucible fired, bathing everything in a light of pure white, Harbinger seemed unmoved at first, but afterward the machine promptly deactivated as its 'eyes' blinked out of existence. After the pulse bathed the system the Crucible shot out a beam to the Relay in the system which caused the Relay's eezo core to turn white as it's rings rapidly started accelerating. And then it shot out a bright white beam into the distance before the rings stopped accelerating rapidly and then eventually turned back to normal speed, the Relay itself remained white.

All over the Galaxy this happened as a chain reaction destroyed the Reapers, instantly destroying the cycle that had gone on for so long. The war was finally over, and the entire Galaxy was glad it was over.

"I'm calling for evac, we all need some serious Medical help." Shepard said before getting on his Omni-tool.

"Joker we need immediate evac, we're all wounded down here and if we wait too much longer we'll begin to bleed out, I'm activating my emergency transponder so that you can hone in on my position."

"You got it Shepard, I'll have Kaiden and the rest of them come and get you, and then I'll send Cortez, is the war over?"

"Yeah it is, I've had enough, Shepard out." He sighed and sat down, leaning against the console.

"You alright?" Tom asked.

"Yeah, I just don't feel right inside, I feel like I'm about to throw up."

"I hear you, take the remaining amount of Medi-Gel I have, it'll keep you alive until our friends show up."

"Thanks Tom, I owe a lot to you."

"We're in this fight together, and you deserve it after all of the stuff you've done for us."

...

Shepard wasn't more glad to stay in bed this time. He was back in the Normandy's Medbay where he was recovering from several broken ribs and a couple burns, most of them were 2nd degree.

"We'll get you to a proper hospital soon Shepard, for now I'll do what I can." Chakwas said as she applied a light antiseptic to the burns he had.

"Is the war over? I was busy in here when the pulse went off."

"It's over, the Crucible ended it with a big white wave, now I can finally sit down without having to worry about someone asking me to shoot up a couple Reapers or to forge an impossible alliance."

"You've done more then enough for this Galaxy. I believe now you can rest and have a bit more time for yourself, God forbid you deserve it."

"You said it, I think I'm going to rest now." The Commander smiled. It was finally over, the threat he'd been fighting for what felt like decades had finally been destroyed, and now he could rest easy knowing that the Galaxy was now safe.

* * *

 **Kaiden Alenko** remained a Spectre throughout his life and proved very effective at dealing with post war issues, he retired after 20 years as one of the most decorated Spectres in the History of the Citadel. He lived in a small house in Vancouver for the rest of his life.

 **Tali Zorah** was known as a hero throughout her people and worked tirelessly after the war to ensure peace between the Geth and the Quarians, citing that she wanted to honor the alliance Shepard had made between them. The relationship between Tom and her never blossomed completely, but they still took comfort in each other from time to time.

 **Garrus Vakarian** eventually became a hero on Palaven after his service to Commander Shepard became public knowledge, he eventually became the Primarch. There was a statue built of him in Palaven's capital city. He retired 15 years after being Primarch and retired in the same house that his family had lived in for generations.

 **Liara T'soni** continued her duty as the Shadow broker for centuries, using it for good instead of evil while still maintaining the reputation of the Shadow broker, she eventually gave the network to her daughter after 800 years in the business. She made sure that Shepard's sacrifice was always honored in her work.

 **James Vega** was promoted to Commander and saw a great many years of service and was eventually promoted to the Rank of Admiral, and was respected about as much as Admiral Hackett due to his service with Shepard. He retired later after 25 years in the service.

 **Steven Hackett** retired 3 years after the end of the Reaper war, he died of old age and was give a Military burial with full honors, the Funeral had over ten thousand people attending including Shepard and several other war veterans.

 **Jeff Moreau** retired soon after the Reaper war where he lived on the Citadel for 30 years. His condition was eventually treated due to amazing advances in medicine after the databases of the Reapers were found, he lived with EDI until he died and although he never had a true marriage, citing he felt it would be awkward to have one, he still had a loving relationship with her.

 **EDI** stood by Jeff Moreau until he died, and continued to serve in the Alliance for many years afterwards, and although she as never really recognized as a member of the Alliance she was treated as one. She served on many ships throughout her service.

 **Karin Chakwas** opened up a private Medical Clinic on Earth where she worked for years until she retired, every Alliance officer was given free treatment. She never married and died peacefully in her sleep one morning.

 **Samara** died fighting off 5 banshees at once to buy time for several shuttles full of Civilians to escape. There was a statue made in her honor in the same city where she died fighting.

 **David Anderson** was heralded as a hero throughout the Alliance after the Reaper war, there was a statue put up in London in his honor. He retired following the Reaper war along with Commander Shepard. He had two children with Kahlee Sanders and lived a full life after the end of the war.

 **Jack** continued teaching in the Academy following the Reaper war, where she was eventually promoted to the headmaster after years of work and never retired, citing that she'd teach until she's drop. She died in the middle of speech and was buried by her students in the Academy, she was known as a Legendary teacher throughout the history of the Academy following her death.

 **Jacob Taylor** had 4 children, one of them was named Shepard since his wife insisted, he came back into the Alliance for a while after the Reaper war and retired as a Captain 10 years later to take care of his kids.

 **Urdnot Wrex** soon became the Counciler for the Krogan and represented them well for centuries, Eve was always there to keep him level headed and he kept good control over the Krogan for a long time.

 **Miranda Lawson** married Shepard after the Reaper war, they lived happily in Vancover in wealth and luxury due to the immense wealth her father had. She helped dig up the remaining Cerberus locations after the war ended which the Alliance promptly investigated.

 **John Shepard** was heralded as a hero throughout the Galaxy, there were statues all over the Galaxy to commend him on his amazing service during the Reaper war, he had two children with Miranda and lived in America until he died. He lived off of Miranda's immense wealth and the royalties of the vids, he died with a smile on his face one morning. Over 1,000,000,000,000,000,000 people watched as he was buried at his funeral and the entire Galaxy mourned his death. He was known as a legend for centuries after his death.

 **Tom Fisher** became a white hat hacker for the Alliance and helped to make amazing addition security measures against hackers for the Alliance. He made a lot of money and retired after 20 years in a modest house near his original birth place in Manitoba. His secret of being from the past died with him and no one besides Tali and Garrus ever found out.

* * *

A/N: So that's it then, Shepard finally got the happy ending he deserved and Tom was successful in preventing the Reapers from giving Shepard a sacrificial victory where he died. I never thought I'd make it this far, I just thought my story would just died, but you guys kept it going, thank you for all the support, it's been a long ride and I certainly enjoyed it. I will no longer be responding to reviews besides send you a PM, thanks again for all the support. This is the end.

Reviews:

 **general-joseph-dickson:** I hope this chapter brought as much enjoyment as the previous one..


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